My son had a 99... strong engine, pretty much bullet proof with basic maint. As far as the piston goes, no it does not had to burn a hole the the top to be lean. How does the cylinder walls look, and scarring or scratches? How about the head? While its down, clean the power valve. One tip if you disassemble the power valve for cleaning, take pic's and notes as to its settings... (don't make the same mistake as me and take it apart and forget how it goes back together)
If all is well, get a new piston, ring(s) and top end gasket kit. While your waiting for parts, takes the time to pull the wheels, re-grease the wheel bearings, swing arm bearings, etc. Go over the bike looking for loose or missing bolts / nuts. Be prepared to replace some nuts and bolts with the correct hardware. Its all part of resurrecting a bike... Now is the perfect time to go over the bike to make sure all is correct, and when ready she will reward you by putting a huge smile on your face.