I've just done my gearbox (850 MkIIA) and was hoping to do it in the bike, but there was no way I was going to get the bearings out without damaging something. I took the gearbox shell out with the bike on the sidestand by removing the rear isolastic bolt and the top and centre bolts holding the cradle to the crankcase. The cradle was then dropped down with the swingarm still attached, pivotting on the slackened bottom cradle bolt until there was enough space for the shell to clear the back of the crankcase. The oil filter had to come off, I took the exhausts off to improve access and there's no centrestand fitted to my bike, but everything else stayed in place. I wrapped a length of rope around the engine & frame downtubes to stop the motor falling back - not sure if this is necessary, but better safe.... Above all, use common sense and watch out for the rocker oil line if it goes inside the cradle! Refitting was easier than I expected, but clearance is pretty tight with a complete 'box instead of an empty shell.
I fitted the Mick Hemmings recommended layshaft bearing, which seems to be a ball bearing with a very substantial non-metallic cage. Incidentally, the bearings were really tight in my shell, but just fell out in the oven at 250 degrees F. New ones dropped in at the same temperature - no need for force at all. No way could I have done this with the shell in the bike.
Hope this helps
Mitch