I have a '95.
Fresh top-end (cast piston). Boyesen RAD valve, flywheel weight, down 1 on the pilot and 2 on the main but I think you have a different carb. Pro-Circuit Platinum pipe and FMF turbine core2 I think with the spark arrestor. I run it 30-1 per the manual and make sure I am running 95+ octane as it WILL detonate with less.
I have tried ATF, gearsaver and 10W40 motorcycle oil in the tranny and the 10W40 is by far the best choice IMO. No false neutrals and much smoother clutch operation and shifting.
Check for wear on the waterpump drive gear. It is plastic and can/will wear out.
Suspension-wise, I replaced the fork seals and the fluid. Set it to stock specs and tuned from there, the rear shock is stock with a fresh recharge and again, set to stock settings and played with it from there. I did not deviate much from stock as my (lack of) abilities were in line with the factory settings for the most part.
Stock gearing. Good bottom end with a big HIT in the mid and a decent top. This bike pulls hard.
So far it has been bullet proof as their reputation has shown.