You can go to
http://www.yamahasportsplaza.com/
and look at the microfiche to see what is all envolved with the seals on the water pump.
On my 2002 it was leaking from the weap hole behind the water pump.
On mine I have replaced the acutal mechanical seal 2 times with the motor in the sled, and it still leaked, I did what is listed below and fixed the problem.(might have missed a few steps) Might also have the impellar itself wore causing it to leak. Once you get it clean, put the impellar on the shaft and see if it has to much play.
Pull the pipe
pull the y pipe
remove the drain bolt on the top right side of water pump cover.
Remove engine mount
Remove the coolant lines from the water pump cover housing.
Remove all bolts from water pump cover.
Remove impellar bolt, and washer
remove impellar
Clean bolt/shaft/impellar threads
ReInstall using removable loctite good foor water application and a
new water pump bolt washer/new seal on the back side of impellar. Use the loctite on the impellar thread/bolt threads/bolt washer. Let sit for 24-48 hrs before adding coolant.
Be sure to bleed all air out of the system by using the screw on the rear cooler and the one on the housing on the cyclinder head. By opening the screw on the rear cooler and raising the rear of the sled, and adding coolant to push out any air in the system, then CLose screw, raise front of sled, open the bolt on the cyclinder head(on top ot the thermostat housing) and add coolant till it pours out of the air bleeder.
Start sled check for leaks, feel all coolers to make sure they are getting warm.
