Okay, so let's think about this. To install the tranny mounts, you would have (1) unbolted the existing mounts (2) jacked up the tranny (3) removed the existing mounts (4) put the new ones in (5) torqued the bolts down to the proper specs [riiight?

]
So things that could have gone wrong could be (1) bolts not torqued to spec, so whole tranny is moving around (2) by jacking the engine and tranny together you damaged one of the motor mounts - assuming they were not loosened to do this work (3) you pulled the driveshaft [front-to-rear] too far and either bent it or damaged the seals/bearings it goes into (4) you damaged the U-Joint on the driveshaft [front-to-rear] (5) you bent the oil pan for the transmission, and the transmission oil has leaked out, so now your transmission is empty and dry gears are not good (6) the driveshaft pulled out of the rear differential and it's drained it's oil so now it's dry (7) pigs can fly [are you still reading all this?] (8) you cracked the transmission case and now it's leaking.
Okay, so it sounds like you should check for leaks, and then you should try and isolate the noise.
Does the car make noise when you are :
1. Accelerating? What gear(s)?
2. Cruising (under light throttle)?
3. Coasting (no throttle)?
4. Braking?
5. Turning?
6. Coasting in
Nuetral?
7. Idling?
8. Driving through puddles?
9. Cold or hot engine temperatures?
10. Cold or hot weather?
11. Full throttle?
12. Clutch in, out, engaging, dissengaging?
So get some more information and we can probably narrow this down.
Of course, if you are in nuetral and the noise persists, it's probably not the transmission, but it may be the drivetrain. If it only happens in gear, then it is the transmission. If it only happens when you are going around corners, it could be CV joints or your differential(s) [unlikely IMO]. Etc.
Get back to me, let me know...