I have a 2003 TE610E, which is the same bike. My bike has a slight surge at around 30mph, which I was told was ECU related, but runs fine at 3500 rpm. I can't find my jetting notes right now, but basically you need to upgrade to the same jetting specs, as a 2000 TE610 left kick enduro bike. On the Dellorto, the AB nozzle is important. At every gear the bike misses only at 3500 rpms. We think its the cdi box.
I posted in another thread about this. Tom at Moore and Sons told me to go to a hotter plug (7) I am somewhat stubborn, but I followed his advise, and it cured that surging that you describe almost completely. It is not your CDI box. If you find the jetting that works (or the specs for the left kick 2000 enduro) post up! I was thinking of going one up on my idle jet to improve the starting issues, but my fuel range is already too short....I am afraid it would become unusably short!
