Awesome build thread!
I'll be doing the same thing to my 2002 soon as well.
A couple of recommendations from your original list:
SeatConcepts for new foam and seat cover
Leo Vince slip-On to replace the OEM Supertrapp (sounds great and half the weight)
Real hand guards
Re-build water pump & check cam roller bearings
Check to see if main shaft bearing has been upgraded
Mugara Jack hydraulic clutch kit
SuperSprox rear sprocket and RK chain (if you do a lot of tight trails get a 15 counter sprocket)
SealSavers (my seals would always get dirty and weep without)
Rally Risers handlebar risers from Rally Connex
Loctite every bolt you re-install...
Re-build BST or better yet install FCR
Cover inside of skid plate with foam tape, helps with noise a bit
Dam these bikes can get expensive...but fun!