Hey SC,
I just went through a 99 kx250 a few months ago for someone at work, once you get the piston /crank/bearings sorted, look for excessive play in the powervalve parts.
The bike had been rode hard and put away wet, (Heck it was 15yrs old!) the clutch basket was pretty well notched and the fibers were burnt.
I'm sure you will have a good look at all the internals, as we also had to replace third gear and several bearings and seals.
My buddy had ordered a bunch of parts before I had gotten the engine torn down and ended up in a budget pinch.
The forks needed seals and bushings, the swingarm and suspension bearings and seals were toast and the throttle was falling apart along with the cable. Brakes and rotors oy-va... I guess what I'm saying is make sure you have a good final parts list before getting the "Goodies."
All I did to the engine was cleanup the casting flaws,roughed up the intake and matched the ports.
(The sizing of the ports were a few mm's off and it wasn't done on purpose) .
There was probably 3mm or so of play in the main valve and the exhaust barrels would not line up correctly no matter how I tried to time them.
We had to replace all the powervalve parts, My buddy couldn't understand how only a few MM's could make such a big difference, until he rode the bike with everything working...
He had a steahly flywheel weight, Boyesen superstock reeds, aftermarket air filter and an fmf pipe and silencer.
He did say he was gonna change the gearing as the stock set-up was just a little to fast in the woods we have around here.
Sorry to prattle on...
Blaster & Foxx have a lot of experience and both stand up guys, their word is good as Gold.
Tuck\o/