Transmission noise...

So just put a fresh motor in my 99 XJ 5 speed, AX-15 trans with a 2 year old rebuild.
The issue im having is in 1,2,3, and 5th gear it vibrates/buzzes, I can feel it through the shifter, and it is really loud in 5th. 4th gear it is quiet and smooth. trans mount is a year old, new motor mounts also. new clutch, flywheel, pilot bearing, and throwout bearing.
Any ideas?
:repair:

It's in the trans, most likely the counter shaft bearings. No noise in 4th is the tell take, since that gear is direct drive and the input shaft is locked to the main shaft.

Im guessing id have to tear down the trans to fix that? the weird part is it didn't do it till I replaced to motor

So I took a good listen to the T-case with it in neutral and the sound is coming from the transfer case. any ideas?