Mr.Torque,
If I were in your position, I would locate a stock or FMF Gnarly pipe (stock will be very inexpensive) for a 1999 or 2000 model as any other pipe moves the power up the RPM range. I have tried just about every pipe out there for the KX250 (DEP,SPES,FMF,ProCircuit,Dynoport) and always end up running the FMF fatty, which takes away a small amount of bottom, but yields great mid & good over rev (not a woods type pipe). If you have access to a dyno, you should see similar results, & just by turning the base of the cylinder down (retarding port timing)& rechamber the head it will add alot of bottom and take some off of the top. You can also take away some of the hook (angle) in the rear transfer ports to add even more bottom (& take away top). If you run across a 95 KX250 cylinder that would be even better as they had very small ports, especially the exhaust, and can be turned into little tractors (with no top end). Keep us posted on the build as I am looking forward to this build.