As Trullion says, first ting to do is check the oil. I had a lot of 'metal flake' effect in mine, and on the magnetic plug, some of the bits were up to 2mm wide, and around 5mm long. Sounds serious, and it looked serious, but as I said, it did fifty thousand plus miles before I decided to strip it. I made that decision because for a couple of months a new silly noise had made itself apparent; a sort of 'groaning' sound, just as the clutch engaged.
One thing I discovered when I had the box off, was longitudinal play i.e. a
lot of end float, about 2mm, on the input shaft. As tapered roller bearings work on a slight pre-load, there shouldn't be any end float. Not sure just how you'd check this wit the gearbox in situ. It would mean a swing arm off job, and remove the clutch activator, thrust bearing and actuation rod. You'd then need something to grip the end of the input shaft, possibly internally in the actuator rod tunnel, and try pulling/pushing. Any movement would not be the best news you could hope for.
I didn't find it
too difficult to replace the bearings (by the way, one each end, it could be either; it was the rear one on mine*, but I replaced both), but I did need the help of a mate to remove the inner cone from the shaft, and the help/advice of Steptoe for removal of one of the outer cones (front, I think) which sits in a blind housing.
It's nearly a year since I did mine, but I'll try to remember what I can, including the fact that I still owe my mate a bottle of Wood's 100 for his help...
Dave.
* Just had a look at an input shaft. They have a helical gear at the rear end. The rotation of the shaft would tend to put pressure on the shaft towards the rear. If a bit of play developed, this would become a slight 'hammer' action on the bearing surfaces when the clutch is engaged, especially if you're a bit sharp with it. Do you have a slight 'clunk' just as the clutch engages? I seem to recall I had. So, as for which one is knackered, I'd say the rear. But the front one will have been running loose as well, so replace both. I got mine from a bearing factors, cost about twenty-two quid for the pair.
Another edit: You say Steptoe mentioned a bearing that can be replaced without removing te box. The only one I can think of is the 'thrust' bearing behind the clutch actuator arm. I'd ask Steptoe if he could clarify which one, and do that before you take any notice of what I've said, his knowledge of GS's is many orders of magnitude above mine...