I have an 01 400ex and it has the factory size tires on it and I'm going to buy some hole shots. I was wondering what is the benifit if any of going with anything other than the stock sizes? What are the pluses and minuses of 4 & 6 ply? Any ideas would be appreciated.

 

yes size does matter lol the taller the tire from the stock size the higher the gearing will be which means you will go faster in the long run but it may take a little longer getting there and a smaller tire will lower gearing which will make go slower but you will have great acceleration.
a taller tire will also give you more ground clearance.

4 ply is a softer side walls and will puncture easier than a 6 ply but the 6 ply will weight more than a 4 ply so if you don't care if you add a few extra pounds go with the 6 ply. and the size its totally up to you but i don't think you would want to go any taller than 22 inches in the back with out a sprocket change.

my cousin has a 400ex with 22inch tires and he has a smaller rear sprocket which gives higher gearing too but with stock sprockets it pulled the 22's pretty easy.
hope this helps you.