Bobt250 is right on about the suspension thing. This is the limiting factor, particularly when dealing with rocks. The motor is good. A flywheel does "mellow" it a bit (in fact I use one for woods and MX). As for the pipe, and this is just my experience, don't waste your time and money. The stock pipe on these bikes is as good as it gets, particularly for woods riding. Better spend that money on the forks (revalve). Extra exhaust gaskets (the little metal o-ring, between the pipe and cylinder) do help gain a little bottom end. You can stack 3-4 easily, they cost virutally nothing and can be removed if you don't like the power. A bigger tank would be a nice addition, as the range is not great, but this is minor.
Summary....suspension, suspension, suspension (particularly the fork).
from a 2000 CR250 owner/rider