First the general info:

My 1999 KLR650 was running hot all the time, and the fan was not cooling it down very well, even at idle.  Eventually, I popped off the water pump cover and found my water pump's impeller shaft was broken.  The nut was still attached to the severed end of the shaft.  Great.  I had probably over-torqued it last year.  -->

First, I tried what others had done successfully and set out to drill and tap the broken end of the shaft.  A 4mm screw could be used to clamp the impeller back in place.  A quick, easy, inexpensive fix.  Alas, not to be.

After flattening the end of the shaft, I drilled it and started tapping it out.  I used cutting oil to ease the process, and backed the tap out regularly.  I may have bottomed out the tap in the hole, though.  The tap snapped off in the hole, and I knew it was worthless to try getting the broken piece out.  I would need to replace the impeller shaft after all.

The impeller shaft is press-fitted into the end of the front balancer shaft, and the whole unit must be replaced ($66 for the shaft).  The manual directs dismounting the engine and separating the crankcase halves.  I was fortunate to have the advice of those who knew that this was not necessary.  After a few helpful suggestions and some examination of the engine and the manual, I decided to remove the shaft without removing and splitting the engine.

I was a bit concerned about removing the balancer shaft.  If it was tightly fitted to any gears or mechanism inside the engine, I was afraid that it would be hard to replace the new shaft without disassembling the engine case.  Fortunately, this was not the case, and the shaft came out easily.  Nothing engages the shaft in the crankcase; it’s only there to drive the sprocket and balancer weights on the outside of the crankcase.  The replacement shaft went in just as painlessly.

Since the process of driving out the shaft puts lateral pressure on the inner race of the right side bearing, I was advised to replace the bearing.  I did so, but I honestly believe that the bearing could be re-used without worry.  It came out with almost no resistance.  I had already bought a replacement, so I used the new one.

The manual requires using some new parts during this process.  Things such as o-rings, snap rings, and washers that get folded over should be replaced.  High torque items, such as the rotor holding bolt also should not be reused.

I followed the manual and the previously published work of others (procedures on replacing the balance tensioner shaft lever "doohickey", oil screen cleaning, etc.) to get to the new work that I hadn't done before.  It helped that I had already been through these procedures, and the familiarity sped the early work.  Once I was at the point of removing the balancer weights and sprocket, I had to refer to the manual.  I won't attempt to recreate all the excellent work posted online for the disassembly up to the shaft replacement.

Do take at look at these procedure guides:

www.multisurfacemotorcycling.com/klrpage/oilscreen.htm  (removing the right side cover and cleaning out the oil screen)
www.devonjarvisphoto.com/posted/KLR650/doohickey/index2.html  (the doohickey upgrade)
http://klr6500.tripod.com/links.htm         (another doohickey upgrade in the Procedures list, on the left side of the page)
http://www.klr650.marknet.us/wpump.html  (waterpump and cover work)

Total cost (including some unnecessary parts that I ended up not using) was about $160.  It's hard to estimate actual cost, since I had several parts (gaskets, snap rings, o-rings, seals) laying around, left over from a bike rebuild last year, and because it's my nature to stock more parts for the “next” job.  I used RonAyers.com for parts, and they had everything to me within two weeks.
 
Work time was about eight to ten hours, a lot of it spent scratching.  I did take my time over a couple days.

FRONT BALANCER SHAFT / IMPELLER SHAFT REPLACEMENT FOR PRE-'08 KLRs
 
This procedure was for my 1999 KLR650 A13.  Earlier models have some different parts, and 2008 and newer KLRs may or may not be the same, so be advised.  I often got "in the groove" during the process, and I failed to take some photos.  I hope I didn't omit anything in my notes.  Consider this article as entertainment only.  There--I hope I'm covered.  Please read the whole document before you do anything.

I used a bike lift.  A lift table would be better, since you could work without stooping or laying on the ground.  You could just lay the bike over, back and forth as you work on it, but that is a lot more work and higher risk of contamination.  It really helps to have access to both sides simultaneously when removing and replacing the shaft.

Okay, onward.

Here’s what we’re dealing with. -->

By the way, the balancer tensioner assembly can be removed as a unit; no need to pull it apart as shown here in the fiche.  Everything after the “doohickey” (as it’s known in some circles) is held together (on the front) by a snap ring.

The front balancer and impeller shafts are assembled as one part, labeled here as 13234.  No way to separate them that I have heard of, aside from massive heat, maybe.

So--clean the bike, drain the oil and coolant, remove the bash plate and any other add-ons you have (such as water pump protectors, highway foot pegs, engine guards, etc), put the transmission in neutral, remove the shift lever and brake lever, detach the clutch cable, remove the counter sprocket cover, and unplug the green neutral-light wire.

Put the engine at top dead center (TDC, page 83 in the Clymer manual).  This will help later if you need to re-align the balancer chain.  The manual calls for TDC so that on reassembly the silver links of the balancer chain can be used to ensure that the weights and sprockets are all in the proper position.

Remove the water pump cover (I left the hoses attached to the pump cover).  Remove the impeller nut and washer, the impeller and the small washer behind it.  There is a small rubber o-ring inside the impeller that you should inspect and replace if necessary.  Removing the impeller over the threaded or broken end of the shaft can damage the o-ring.  It may help to "spin" the impeller on and off the shaft as if it was threaded.  This will allow the o-ring to follow the threads.  It's best to replace the o-ring if you have any doubts about it.

Inspect both faces of the mechanical seal (around the shaft and on the impeller) and replace if they are scored or pitted.  My mechanical seal had separated into two parts that probably still worked fine, but I replaced the seals anyway (I had the parts on hand… packrat me).

Remove the right side engine/clutch cover.  -->

15 bolts, one obviously longer than the others.  My gasket had already been re-used, and got torn up this time.  I had a spare on hand.
 
(The front engine mount bolts are out because I had removed the Dual Star water pump guard (which bolts through the front engine mounts.  Also, I had an engine guard/highway peg mounted over the engine mount brackets.)

Might as well inspect and clean the oil screen, since you're here.  I had just cleaned mine last year, and again there were a lot of gunky bits on it.  This was after I cleaned it.  -->

Remove the left side stator cover and starter gears as outlined in the tensioner shaft lever (doohickey) guides.  Stop there.  You need to have the rotor still in place so that you can use the rotor holder wrench while removing the right side balancer weight. 

To remove the right side balancer weight from the shaft, first flatten out the lock washer, then while using the rotor holding wrench on the left side of the engine, take off the right side balancer weight nut (24mm), washer, weight and finally a spacer.-->
 
This part of the job was new to me.  Try to keep the engine at TDC.  (I kept moving it.)

After you've removed the right balancer weight and spacer, note the bearing around the balancer shaft, and the bearing retainer that is screwed to the crankcase.  -->
 
The retainer must be removed, as the shaft and bearing will be driven out this side. 
 
I had a very hard time removing this retainer screw.  A phillips head?  Are you kidding me?  It was so tight that after my screwdriver partially tore out the X, I resorted to an impact driver (the kind that you hit with a hammer).  That finally worked and the screw came out.  I expected to find it glued in, but there was no evidence of adhesive.  It must have just been in there very tight.

Return to the left side of the engine.  Use the other procedure guides to remove the rotor and woodruff key, starter clutch gear and spacers, and tensioner bolt and lever (doohickey). 

Remove the inner crankcase cover and the remaining balancer chain tensioner assembly including the tensioner sprocket.  -->

The spacer behind the balancer tensioner sprocket often falls into the oil sump, so stuff a rag there first.

You need to remove the balance tensioner sprocket so that the balancer chain has enough slack to be removed from the front balancer sprocket.

You may want to check your balancer chain alignment here (read ahead in this document).  I found my chain was off by a few sprocket teeth.  (I now know that the chain does not align with the landmarks every rotation, so my chain might very well have been aligned just fine.)

Okay, for me, the rest was all new territory.

I found it helpful to remove the two balancer chain guides.  It was difficult to get enough chain movement to remove the front sprocket with the guides in place.  I suppose it would be possible to work with the guides in place, but I chose to remove them.  The screws holding these guides were securely held by what appeared to be red threadlock. 

I goofed (see the oops in the photo below) and also removed one of the cam chain guides, which necessitated removing and resetting the cam chain tensioner unit before I could replace the cam chain guide.  This is the chain guide right above the crankshaft.  I took the left photo (below) after I had removed the front weight and sprocket, before resetting the tensioner.

      

Remove the snap ring from the end of the balancer shaft, and then remove the front balancer weight and sprocket. -->

There is a spacer behind the sprocket that comes off, too.

I took this photo before removing the chain guides.

Once the weights and sprocket are off the front balancer shaft, you can feel how easily the shaft moves left and right through the bearings. 

The shaft is trapped between the two bearings.  (In this photo, I’ve reattached the cam chain guide, but have not yet reset the tensioner, so the cam chain is a bit slack.)

At TDC, the woodruff key slot is pointed upward.  The “T” mark on the face of the rotor that is used to determine TDC is lined up with the woodruff key.  -->

I used a small dead-fall plastic mallet to remove the shaft.  I rapped on the left end of the shaft, and it pushed out the right side bearing with very little resistance.  There is a flange on the shaft that traps it between the two bearings.  It’s this flange that drives out the right side bearing.

Using a 1-½ pound dead-fall mallet, it took only two light raps on the left side.  -->

The shaft driving out the bearing on the right side.  -->

The broken shaft (with the bearing still on it).  -->

This is the broken bugger.

I kept the left bearing in place (you could knock it out from the right side and replace it if you wanted).  I oiled and inserted the new shaft, then oiled and knocked in the replacement bearing.  -->

I had a brass drift ready for this purpose, but after seeing how little pressure was needed to remove the bearing, I chose not to use it.  I used a small plastic hammer to start the new bearing in place.  I then used the dead-fall mallet to strike the small hammer, which I worked around the outer race of the bearing.  It took very little effort to seat the bearing into place.  No damage to the bearing this way. -->

I replaced the bearing retainer, starting it with a large phillips screwdriver, and used the hammer-struck impact driver to seat the poorly-designed phillips screw firmly.  I think it would be possible to over-torque it and strip the threads with the impact driver, so take care if you use that tool.  Otherwise, I'd use threadlock on that screw.

The shaft moves freely between the bearings, as noted earlier.  That’s why it looks recessed in this picture. -->

Put the right side spacer and weight on now.  The balancer/impeller shaft is marked on each end to help with aligning the sprocket end weights.  On the right side, the outer end of one of the splines that the weight slides onto has a dimple on it.  That dimple lines up with the alignment mark (punched dot) on the right balancer weight.  I didn’t take a photo here, but it’s pretty obvious.  Put the lock washer (its "peg" goes into the hole on the weight) and the nut on finger-tight.  It will need to be tightened later, after the rotor is back in place. 

Back to the left side of the engine.

Put the left side spacer on, then the weight/sprocket unit.  The sprocket has an alignment mark (a punched dot) that needs to be aligned with the similar mark on the left end of the balancer shaft.
 
The snap ring goes back on, sharp edge facing in.
 
The snap ring isn’t in place yet in this photo.  -->

The balancer chain has some distinctive silver links (on newer models).  There are two pairs of silver links and a single silver link between the two pairs.  The alignment marks and silver chain links were also marked with paint in my engine.  The paint helped some, but on the rear (upper) balancer sprocket, the spacer over the sprocket was also marked with paint.  This caused me a moment’s anxiety, because the spacer rotates freely, and the paint mark kept moving!  Okay, ignore the painted spacer--got it.  Ditto the paint on the snap rings.  (I now believe the paint marks were just part of the assembler's checking system during assembly.)
 
I found it easier to align the single silver link with the central crankshaft sprocket first (as shown in the photo at right), then align the rear and finally align the front sprocket. The front and rear sprockets can be turned; the crankshaft cannot, so I started there.  -->

The manual says to align the rear sprocket first, then run the chain under the crankshaft aligning the silver link with the hard to find sprocket mark (removing the cam chain may make it easier to find), and then run the chain over the front sprocket with the silver pair of links straddling the alignment mark.  Your choice.

The silver link lines up with a marked tooth on the crankshaft sprocket.  I had a hard time locating this marked tooth, partly because it was on the bottom of the sprocket and I had to lay on the ground to look for the mark--again, a lift table would have been better.  Directly opposite this chain alignment mark is another marked tooth that could be misleading if you weren’t at TDC.  A line drawn between these two marked cogs will be parallel to the cylinder.  Removing the cam chain may make finding the marks easier.  You can’t see the mark in the above photo.

My balancer chain was a few teeth off alignment at the rear (upper) balancer sprocket, so I aligned the sprocket per the manual during this reassembly.  I hadn’t noticed the chain-sprocket alignment during disassembly.

I may have accidentally misaligned the chain when I did my doohickey swap last year.  If so, my engine might have been out of balance this last year.  (Or, as I mentioned earlier, the balancer chain doesn't align correctly with every rotation of the motor, so it might have been fine.)

Again, the spacer has a paint mark (and I lined it up for this photo), but it rotates, so look at the sprocket for the marked tooth and ignore the paint on the spacer.  -->

On the front (lower) balancer sprocket, the last pair of silver links aligns with (straddles) the punch mark on the TOP of the weight, which was also marked with paint. 

The exact location of the punch marks might be different on each part, because the mark on the top of the weight was not directly in line with the mark on the side of the weight.  It wasn’t off enough to matter, though, and that's how it was assembled at the factory.  There’s a marked tooth on the sprocket, too, so you can't go wrong.

Same photo as earlier, without the labels (again, the weight isn't fully installed in this photo).  -->

From the Clymer manual.  -->

Hope it helps (and nobody sues me…).

If you removed the balancer chain guides, put them back on now.  Use red locktight (threadlock).  I had to rotate the front weight (and the chain) to get one of the screws back in.  Be careful not to lose chain alignment if you move the chain.  The larger screws (8mm) get torqued to 18 FOOT-lbs., the smaller ones (6mm) get 106 INCH-lbs.

On the subject of chain guides, I may have to replace mine the next time I’m in there.  The two that I removed had some of the plastic coating broken away, revealing the inner synthetic material that looked like wood (brown, with a grained appearance).  -->

<NOTE>  Since doing this procedure, I have seen the inside of a lot of KLR650s, and many of them had similar wear on these chain guides.  Large bits of the coating had broken away.

This would account for some of the black bits that came off my oil screen both times I cleaned it.  A good reason to clean the oil screen at some point.

Okay, temporarily attach the rotor onto the crankshaft with the woodruff key. 

Use your rotor holding wrench to hold the rotor while you torque the right side shaft nut down to 32 foot-lbs.  I had to buy a 3 ½” deep socket (24mm) for this because the shaft is now locked from movement.

Same photo as earlier, just as useful.  -->

Fold one edge of the lock washer against the nut.

You’re done on the right side.  Clean your oil screen, choose your gasket preparation (or none), and bolt the right side cover back on.  Screws are torqued to ~70 inch-lbs.  (Different references call for torque between 68-72 INCH-lbs.  This seems to be a consistent range for all case- and side-cover/water pump cover screws.)

For finishing off the right side, refer back to the excellent procedure guide for water pump seal replacement, noted earlier.

I was careful to not over-torque the impeller shaft nut this time.  It only needs 88 INCH-lbs.  I didn’t have a low range inch-pound torque wrench last year, and I had to estimate what 88 inch-pounds felt like.  Turns out that I suck at estimating 88 inch-pounds.

Finishing off the left side of the engine was easy enough.  Follow the noted guides.

When I was done and got the motor running, all was well with the operating temperature of the bike.  I couldn’t get the needle past the halfway point on the scale on the shakeout ride.  I had let it idle until warm, then revved it a while.  The temperature needle went to almost half and stayed there without the fan coming on.  I rode it a while (the weather was coolish), and the needle dropped to about 20% of max.  Back at home, it rose back to about 50% as it idled and the fan came on briefly.  I have added a manual fan switch on this bike, and after letting the fan run a bit, the temp dropped enough that I am confident that all is well now.

WOO HOO!

Please email with any help on this document.  Typos, errors, or other stupidity will probably be easy to spot.

Or, you can PM me on KLR650.net, KLRWorld.com, or ADVRider.com.  I’m SgtMarty on those sites.