Try putting the bike on the side stand. The engine moves. If it moves too much, have a helper SLLLLLOOOOOWWWLY take it from side to center stand. At some point in the transition, you should have clearance.
EDIT: I just gave you a GREAT tip for a completely different problem (aligning the bolt holes in the cradle and engine).
I had no issues with getting that bolt out, so I'm completely guessing here, but perhaps with the nut out and the bolt pulled back a little (at least enough to clear the bolt hole on the right side), you can rotate the top of the gearbox to the right side enough to "lift" the bolt path past the frame rail?
Good luck. Best news is whatever you're doing to the gearbox, right up to a complete rebuild, getting the box in and out of the frame is by far the toughest part - the actual gearbox work is a snap.