The spigot bush would affect all gears, and as the first motion shaft is so long, even if it was missing, the impact at the gearbox end would be small. It would make the clutch engagement very jerky though as the plate wouldn't be centralised.
Reverse gear whine does sound like something in the bearings is not too clever, and that would also go for the transfer box gears too, which are helical and biased/thrust one way when going forwards and the other way when going backwards.
My suggestion is the same as James above, drop some oil out of both boxes and see what comes out in the way of debris, I'd lean slightly towards a tranny box problem.
Peter