clunk noise from trans when shifting at low RPM

[nep]

i recently did a auto/manual conversion on my 96 240sx. everything was replaced during the swap, including master/slave, T.O. bearing, clutch fork, etc. my problem is this:

when shifting gears from 1-2 and from 2-3 at low RPM i get a clunking noise that appears to be coming from the transmission area. if i i take it much above 3k rpm the noise goes away and the shifts are pretty seamless. i have done quite a bit of searching and have come away with a few suggestions:

1. drivetrain slack
2. rear end bushings. sub-frame, diff, etc.

i was bored so i let a local mechanic drive it around the block, and his diagnosis was bad transmission gears or some shit, and offered to rebuild it for $1500. that price is ridiculous as fuck, and im hoping my problem has nothing to do with the actual transmission anyway. maybe i need a new driveshaft? any thoughts?