I have over 3k miles on my '98 with absolutely zero tranny problems. I had to replace the clutch after about 2500 miles, the alum plates were worn out. I replaced with steel and now the oil comes out looking like new. I started out using Mobil 1 10w30 for about a season then switched to ATF F. I think it shifts better with the Type F and it is so cheap that I change it after every ride.
There was a smattering of tranny problems in the 98/99's. The 99 KTM 200E we have had to have the tranny replaced shortly after birth. Seems most of the ones that went out went out right away. No problems that I've heard of in the last couple of years.
There was a problem with 2000 200s with some part that would come loose early on (hopefully). KTM was fixing these under warranty from the people I talked to, and the problem was not there in '99 and '01.
Maybe dstktmusa can offer more details, or maybe a copy of the tech bulletin text.
a few 2000 model 200s had a shifter return spring or something like that which would pop out of place; ktm fixed them under warranty. my old '98, with thousands of hard riding/racing miles on it, is still going strong with its 3d owner, never a tranny problem. my 2000 has never missed a beat for any reason.
Yes, I already have an 02 but I haven't ridden it yet on the trail. I am planning on ridding it this weekend. What William siad is correct. They also changed the shock but it didn't get the full update like the SX models. A friend raced his 02 yesterday at a Dist 22 Enduro and took the overall on it by 3 minutes on me. He said it worked great and he thought the suspension felt better than his 01.