Since you haven't fixed it yet;
FYI:
with the engine running, and the trans in Neutral,and the TO bearing fully retracted off the clutch fingers, and the vehicle stopped;
the input gear is locked to the crank, and lock-stepped with the cluster gear, which is spinning the three gears on the mainshaft.
The only things not spinning are the synchronizer assemblies and the mainshaft. So the only bearing NOT spinning is the one on the rear of the mainshaft.
As to the cluster Needle-rollers; they are buried in the bottom, and very seldom make noise,unless water got in there.
As to the gears; they extremely rarely make noise; unless you cooked one while towing in a gear other than direct, or something went thru the drive teeth.
As to the needle rollers in the back of the input gear. These too seldomly make noise, unless it was assembled wrongly, or run low on oil and they got cooked.
As to oil: I run 50% Dextron ATF and 75/90 EP, and my trans runs dead quiet.
So, that just leaves the input bearing as the most likely to be noisy.
Since you said it has low mileage on it, and the noise remained after you changed it;
I would drop that bad-boy and inspect it.
