I thought I would share this with all of you because it was a huge learning experience for me and maybe it will help someone else. I would have attached pictures, but didn't think to grab the camera while swearing to myself the whole time...
Here is a link to the diagram and parts list, which I will be referring to.
For starters, the water pump is on the left (kickstand) side of the bike. It has a big hose coming out of it and is partially covered by the clutch slave/cover. Can't miss it. Its major parts include the visible outer cover, an inner cover, impeller w/ shaft, bearing, oil seal, and mechanical seal. If you notice that you are leaking coolant from the pump, really try to locate the leak. My problem appeared to be leaking from the bottom most bolt on the outer cover. The PO replaced the o-ring #7 with instant gasket, so I assumed that was the problem. Replaced it with a new one with no change. You really need to get up under the engine while it is running and leaking to see where it is coming from. Found fluid flowing from the hole that the inner cover mounts to (which is where the wep hole is). This told me that the mechanical seal and/or oil seal were bad.
Here's where I get to the process:
1. Remove left fairing and lower cowl
2. Drain coolant (The drain hole is the bolt on the pump that is closest to the intake hose, almost concealed by it). Drainage is quicker if you remove the radiator cap or open the bottle top of the reservoir. I just removed the hose clamp and hose over a bucket.
3. Drain oil (2 quarts should be enough to allow removal with no spills). As I said previously, the inner housing sits in a 2" diameter hole in the bottom block and if you don't drain those 2 quarts, they will end up on your floor.
4. Remove clutch slave (3 bolts)
5. Remove chain/sprocket cover (don't forget bolt in the center of the cover)
6. Remove all bolts from the water pump. The top and bottom bolts are significantly longer because they mount the entire assembly to the block.
7. Remove the hose from the intake and remove bolt holding the solid output pipe to the block.
8. Pull on outer cover while "wiggling" the hard pipe back and fourth to remove both parts together (an o-ring seals and holds this pipe in place on the top of the engine and in the water pump housing)
9. Now that you can see the impeller and all of the previous steps are complete, begin twisting and pulling on the inner housing NOT THE IMPELLER. It will take a significant amount of force, but twisting and alternating pressure will eventually pop it out.
1. Remove the circular clip (blanking on term) holding the impeller shaft against the bearing (Careful, you will need to re-use this. Go get the $5 tool to spread it open)
2. Remove shaft from inner housing
3. Removing the mechanical seal sucks, it has an adhesive around it and is already a pretty tough friction fitting that you can't pound out because of the bearing. Rip out any springs or caps attached to it, cut the middle of it with tin snips, grab a pair of vice-grip pliers and go to town.
4. On the back side of the impeller, there is a white and black bushing that can be removed with a small screwdriver. Remove and replace it, using even pressure to set the new one fully in the cup
5. use a socket to remove the bearing and oil seal from the inside after the mechanical seal is removed.
6. Replace the oil seal by lubing it up and pressing it in so that it is just slightly recessed or it will rub the bearing and create friction.
7. Tap the bearing back in to place
8. Set the new mechanical seal in place with your fingers and then tap it in with a large socket that fits the outer lip and a rubber mallet.
9. Re-install the impeller and locking clip
1. Place the whole inner portion back in the hole, careful to align the shaft with the gear inside the engine. (you may need to place the outer housing over it at this point and use the two longer screws to help press the inner assembly to a fully seated position.)
2. Place a new o-ring in the grove of the inner assembly (coat it in oil to make it stick to the inner assembly while you work)
3. Insert the hard tubing and o-ring to the outer assembly/cover
4. Simultaneously push the other end of the tube in to the receiving end on top of the engine while setting the outer cover in place.
5. Bolt it all up, fill it with fluid, and admire your leak free bike.
A Few things I almost really F$%ked up:
1. DRAIN THE OIL! I changed mine an hour before I drained 2 qts of new yamalube on the floor.
2. Do not pull the clutch lever while the slave is off
3. Do not run the bike while the slave is off, the lever it presses on will try to eject itself from the engine as oil pressure builds.
4. Keep track of the copper washer on the drain bolt for the water pump
5. well there isn't a 5, but send me a PM if you have any questions.