Are you granny shifting or double clutch/ rev matching?
This transmission does not like to be granny shifted. If you are trying to downshift by pushing in the clutch and holding it there while pulling the shifter down into 2nd, you're doing it wrong... If you don't know how already, research double clutch shifting. Get used to it and it will shift smoothly.
Also get rid of the OEM transmission fluid. I dumped mine and put in Pennzoil Synchromesh and it made a big difference. There are some other recommendations on oil here:
http://www.ft86club.com/forums/showthread.php?t=46208