I've been following this from the beginning, not because I know anything about this transmission, more because I thought I might learn something.
After looking through some of the parts diagrams, it seems I know even less about it than I thought I did. This is a power reverser transmission, right? It has a mechanical directional control valve, operated with a lever and two cables? The clutch pedal controls an inching spool within that control valve, and there are no electronic components involved at all? That sounds like a carryover from 1980's technology, the sort of thing I remember from the first wet clutch pack tractors I ever worked on.
If that is indeed the case, I must assume you have looked at all the external parts of that package and found nothing suspicious? I wonder is the noise only present in forward and not in reverse?