Change out the carb to a 36mm. Then to find a straight tapered needle to work with it. It takes some playing around with but it help more them anything else I tried. It's been a few years since I had my 01 TM250E, so I'm not sure what needle I ended up. I think the biggest problem with the 01 'E' is the tranny, the wide ratio 5 speed seem to kill the low end. 1st gear seems to be fine in the real ugly stuff but the jump from 2nd and 3rd gear seem to take alot of clutch work. You may want to look at tring to change out to the 5 speed MX tranny.
Best of luck.
brown