you said the bike is totally stock, right??? did you blow the motor up already? if so then yes i would change the pistons, and use the wiseco pistons. if you haven't blown up the top end then i wouldn't tear the motor apart just to put pistons in. you aren't going to notice much difference in a totally stock bike.
i would suggest getting a good set of pipes and silencers first. then when you have to tear the motor apart then change the pistons. you know the old saying if it ain't broke don't fix it... i think that applies here. good choice on a quad though.
my 2 cents and you can keep the change.