T1,
I have the 03 200, I love it. I am running it just as it came from Lansing cycle. I did put the 46 tooth rear sprocket on though. My bike is chrisp, and pulls hard. I think that it would pull a 44 tooth rear real easy. I hardly ever use 1st or 2nd gear. It has to be real tight to get in to 2nd.
From what I understand KTM mellowed out the 200 in 04 and from riding Smitdog's bike it would seem to be the case. His bike was smooth and very nice. But stuff that I would ride in 4th on mine I was in 3rd with his, and it lacked that snap that I have. I have not ridden his bike since he added the mods to it though.
I read where you were looking at pipes, I believe the stock 200 pipe is so close to the FMF gnarly pipe that it is not worth the money to switch.(old ktmtalk threads on pipes) Guys that were putting pipes on were getting doma pipes. I really don't know what EE has for the 200.
Jetting can make alot of difference, I have never had to mess with mine, thanks to Napper.
I only wish I had another 20mph in it on top end.
I would ride it for a while and see if you get used to it before dumping tons of money into it.
Brian