Some of the gears have a sort of copper plating which looks brown after use. It’s nothing to worry about. What sort of mileage is the bike? I’ve never noticed gear wear as a problem, but I have had a few break a tooth.
Third & fourth are near the middle of the shafts, so I would not expect bearing noise from them – more from gears which are nearer one end or the other, first and fifth. Then it might indicate damage to one bearing or another.
If you’ve got the engine apart why not replace the bearings anyway? That’s what I always do. Engine rebuild – all new bearings and seals. Look for respectable bearings like SKF, FAG, NSK, and make sure they are the correct clearances, C4 for crankshaft and C3 for gearbox, as detailed in the manual. The clearances matter, and proper fitting, again detailed in the manual.