No need to pull the motor.
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.
I have replaced the acutal mechanical seal 3 times with the motor in the sled, and it still leaked, there is a thread on here that stats what I wrote above about how to fix the water pump weap hole leak. I just did waht is stated above last week and fixed the problem.
http://www.totallyamaha.net/forums/showthread.php?t=60877&highlight=water+pump
http://www.totallyamaha.net/forums/showthread.php?t=61644&highlight=water+pump