I am rebuilding my friend's '01. The bike is way too rich for the riding in the elevation (5,000ft). The carb is a mikuni, and I've heard of some people machining the slide to help dial the carb. I'm looking for a reference point with the needle, pilot jet, etc.
I have one of those bikes. I run a 15 idle jet, an S-7 needle jet (you buy them from your yamaha dealer), a 6BEH1-76 needle on the second clip and about a 380 main for altitudes around 5000.
FYI the S-7 thing is the nozzel, i.e. part the main jet screwes into and you can get them from any dealer that is a sudco distrib (virtually all dealers are sudco distribs). I'm at lower altitude so my specs will not help you much.