It appears you have a kick start 5 speed. So this would be a 1974 5 speed maybe? Do you know?
You say there is an X on the input shaft? Where? I mean where is this X. If you are thinking these might be X gears, they might but the X is on the angle cut gear only, not on the shaft.
To get the other shafts out heat the case with propane torches. Usually use two torches because it takes a lot of heat. I use Mapp gas in my propane torch it burns hotter. If you have Acetylene you have to be careful to not get the flame too hot and melt a hole in the case. Heat the case with the opening down and the shafts will fall out.
The blackening on the bearings is not a problem. Check bearings for lateral movement, looseness. And roughness.
You should be prepared to reshim this box but did you catch the shims that were in it so you know where they were?
The noise you describe sounds like it's from the clutch. Was it louder when driving or just at idle?