I’ve recently swapped my 5 speed manual transmission due to wear and tear from previous owners. It popped out of gear, sometimes would struggle to go into 1st, etc. I also heard a lot of noise as if it needed clutch bearings but i know that wasn’t the case because about 4 months prior i changed the clutch (STG2) & bearings. Anyways, newer transmission, same clutch with about 4 months worth of wear. With a cold start and drive, i have no issues. But after a few miles, shifting from 2nd to 3rd it grinds for about a split second then goes into 3rd. From 3rd to 4th i also feel
some resistance. I also still hear a bearing like noise when the clutch pedal
isnt pushed down. Could this be the clutch or possibly the torque converter? I’m sure it isn’t the transmission

 

There is no torque converter in a manual transmission application. It could be the release/throw-out bearing, or something still inside the transmission.