Since the lower housing is working correctly, and there were no previous problems before the rebuild logic would tell us that there is something wrong with the new parts you put in. New synchros take a few miles to wear in good, but that should not be the main cause of your problem. The transmission on my 44 mb is still a little tight from rebuild but it gets better with each drive. However, since the problems come and go, nobody can tell you for sure. I would investigate that new sift fork next, like Mr. Beep said.
Great job, don't feel too bad about the bugs, they are present with every major rebuild. Its a great feeling to finally get them worked out.
82 Black SL