I have a '94 1100 (although it had a warranty replacement M97 box at some point in its early life). When the input shaft seal failed last year (happily just <i>after</i> a 3000 mile trip to the alps), I sent it to Steve Scriminger for a rebuild (new bearings and seals throughout and anything else it needed). When I got it back I noticed that it was much quieter in operation (still a Massey Furgerson gearchange but that's normal for an M97) however the whine that I'd thought normal has gone.
I can't know how much of this noise reduction is due to the new bearings or Steve's care with preload (he also centres the preload rather than shimming from one end), but I ran the box with its whine for 25k with no ill effects - it did get very gradually worse but it's hard to quantify as you 'get used' to noises. My first couple of gearbox oil changes were quite dirty and had slight gold speckling in the oil (indicative of selector fork wear - and sure enough it needed a replacement fork during the rebuild), although paradoxically, the last few changes were always clear - I change all fluids every 3k, so the initial dirty oil might just have been residues from its earlier life.