Follow my advice at your own risk.

It helps to think about how the m/t works to diagnose it by sound. I usually get some of this wrong, so chime in with corrections. Rotation comes in the input shaft, which spins on bearings on the upper shaft and in the front bearing retainer. It can be locked to the upper shaft via a syncro, or the syncro the other way locks it to a gear that spins on it and is engaged with the lower shaft, which is all one piece with 3(?) gears on it (the countershaft), and the gears on it engage gears on the upper shaft. 1st, 2nd, 3rd, and 5th work by the torque going to the input shaft, the gear that spins on it engaged with the c/shaft & gears, and by locking the appropriate freespinning gear on the upper shaft to the upper shaft with a syncro. All gears are always engaged, by only one set is locked together at a time and to the upper shaft which sends the torque out the rear. You get 4th when the gear to the c/shaft is freespinning, and the syncro locks the input shaft to the upper shaft, and thus to the output shaft. Reverse uses a gear train to reverse the rotation of the output shaft, and reduce the rotation rate.

4th is the quietest gear, because there's no gear reduction going on, just shaft spinning. The input shaft is also locked to the upper shaft, so any runout there is reduced. That's why I could drive mine home with a blown input shaft case bearing. Gear noises in 1,2,3 & 5, and ususally R are signs the bearings are going, or a thrust plate is too worn, allowing too much slop in the tapered roller bearings. Bearing preload (to keep the "cones" of the taper roller bearings tight, and the shaft aligned in the process) is controlled by shimming the thrust plates/bearings so that the tapered roller bearing cone slack is taken up, plus a hair. Once that tightness is lost, the bearings don't last long.

If you have the tranny out, or the engine, grab the input shaft and see if it moves in/out, and/or side to side, to any degree at all. You should have no in/out that you can feel by educated hand, and only perhaps .5mm side to side (that gets controlled by the crankshaft pilot bearing). Any more, and you need to fix it now.

If it starts making noise, I'd fix it now. It only gets more expensive to wait. Bearings, seals, syncros, thrust plates, and shims, are LOTS cheaper than shafts and gears, especially if you weld the input shaft to the upper shaft, or eat off the front end of the upper shaft, or crack the case, or....

Build it right, lube it right, and the 5spd will live quite a while behind a carb 2.6 or v-6, both of which only put out around 150-175 ft lbs of torque.