Same for me recently. Noises in 2nd and 3rd. But 4th was quiet, because it is direct drive. I took the trans out and took it to the trans shop for servicing..
It was bearings and shafts and synchros. but the gears were fine! It got sort-of expensive. I guess I could have done it myself, but just wanted it done quickly.
Sounds like yours has got to come out.
I replaced all the clutch parts while I was in there, too.
