Dan, the power is good on the '01 and if I remember in '99 it was good too. This year the cylinder was changed to add/redesign the ports for more power, and I think the ignition is new too. I don't know what changed from '99 to '00, but all three years the bike is similar and parts should be pretty much interchangeable. It would be expensive initially to get a new ignition or cylinder but if that was all to solve the problem it would be worth it. I will try and dig out last years reviews on the '00 and see what they recommended for fixes. You can always get a pipe like the FMF Gnarly, or a RAD valve which will probably help a little. Good luck with the bike!
The easiest way is to change the exhaust system. There are many options: FMF, ProCircuit, SPES, Dynoport, and KTM hardware(from KTM used on World Enduro bikes), Acerbis (E35 is a very quite unrestrictive muffler/SA). Note that KTM hardware has quite a few aftermarket parts designed specifically to customize your KTM to your liking.