Leaking coolant

This is very common on the yfz. You'll notice coolant coming out of a little pipe on the bottom of the water pump. As long as you have noticed its leaking before its ran dry its ok, as its usually a seal that has perished or the shaft has wear on it and is damaging the seals. Yamaha have upgraded the seals in later year models and these seals fit earlier models. Here is a link to get part numbers for the parts you will need:

 http://shop.thumpertalk.com/oem.asp?partcategory=284219&manufacturer=6&category=1&year=2005&model=6888

I replaced the two seals 6+7, shaft 3, bearing 8, and all gaskets and o rings.
I didnt order the parts through thumper talk i just took down all part no's and ordered through a local motocross shop which were a lot quicker to deal with than yamaha dealers, All parts were oem yamaha.