I used to just sand em a bit when I ran into that, but also that problem can be caused by the wrong amount of trans fluid...I dunno.
I have noticed that using ATF seems to make the problem worse, perhaps due to it's different consistency.
I use 220cc's of straight motor oil, and really, have never have shift problems with any tomos other than the Silver Bullet, and that was cause one of the clutches was a bit worn.
One trick to master with Tomos is a quick wrist-flick on the throttle.
As yer Tomos approaches the shiftpoint...when you've ridden it long enough to know the exact timing of it, one ultra-quick snap to half-throttle and back will cause it to shift nearly instantly...you time it right and you'll slide from first to second smooth as glass.
The key is knowing yer 'ped really well, and knowing exactly where that "breakpoint" is by sound alone.