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Anyone know why my transmission makes noise in all gears except 4th (direct drive)? Seems noisyest in 5th gear, Also a little noisy idling in neutral and quiets with the clutch pushed in.
Pilot bearing looks good
Clutch Release Bearing seems noisy when spinning free, but should it spin while driving (disengaged)?

81 corolla donor- rebuilt 3tc, T50 transmission inspected, new clutch kit, and transmission tail swapped with an early model to move the shifter 4" forward. About 6k miles on drivetrain.

I think you just diagnosed the problem all on your own. "Clutch Release Bearing seems noisy when spinning free, Also a little noisy idling in neutral and quiets with the clutch pushed in."

I wasn't sure if the Clutch Release Bearing would be spinning when not used.
The more I think about it the ONLY bearing not spinning in 4th (direct drive) is the 12 roller bearings coupling the input shaft to the main shaft.
Upon inspection I can't see anything worn, scratched, or scored. No metal debris anywhere

4th gear is the only time I don't hear the tranny rumbling......maybe that's normal?

Im no expert but I dont think a tranny "rumbling" would be normal for any car! I dont know if they spin when not in use, but they do make noise when they go bad. So like you said, it makes noise all the time except when engaging the clutch. Thats how they do.
Can you post a video? I mean putting this on a different car will be kind of hard to know what else it is. I can think of maybe it has the wrong oil grade? Low oil or the tranny is going bad. Another thing could be the driveshaft being shorter with a higher gear pushing the tranny harder and faster. But that would be whining, rumbling sounds like the tranny is falling apart..............

I wish I did record the noise while driving. Whining / rumbling can be subjective. To me, whining is higher pitch and rumbling is lower pitch. My noise is kind of in the middle.
What puzzles me is why there isn't any noise when driving in 4th gear.

Jeff at Toyz Unlimited gave me a tip to use a vice grip type c-clamp to put stress on the bearings. Sure enough the input shaft front bearing (not pilot) got rough to spin with little pressure.

Now to find the bearing......it looks like Nachi 308c87s13n is stamped on it. I can't find anything to cross. Only ones I see for a t50 is National Ball Bearing Part No. 304-L (countershaft) & 305-L (output - rear)

Where do you put the vice grip?

on the sides of the bearings. the clamp has little feet that pivot and just get them 180 deg. on each side of the bearing.
The input bearing to the front case (not pilot) got jerky with a little pressure and locked with moderate pressure. All other bearings spun equally with no to moderate pressure. I never heard of doing that, but it works great.

Now to find a replacement.

Please let us know if you find a new bearing and source to buy it from. I think mine is going out too.

There may be 3 bearings being shipped from Australia to NC. If they are the right ones and get here soon.
Another option I'm considering is a Nachi 6206n bearing (around $10.) 30x62x16 and getting a sleeve made. My original is 30x68x16
http://www.nachi-fujikoshi.co.jp/eng/ji ... 59-166.pdf