You should also take into consideration whether or not the shift shafts on those Yamahas have been changed. If not, those will be a major expense to replace (it's inevitable, the question is when) and often times that cost is more than the motors are worth if you are paying for labor.
I ran across this site one day that advertises aftermarket shift shafts. I don't know of any that has actually used them though.
http://www.shiftshaft.com/