You won't break the cylinder studs by turning the engine upside down. Plenty of people flip the engine over and rest it on the studs, with no issue. Put it on a piece of plywood or something, so you don't ding up the threads at the tips of the studs.
also +1 to the above flipping the motor around to see if you can get the nut to fall out.
If you DO split the cases, Do NOT use any old RTV on the case halves. Use Hondabond or Yamabond or a similar product specifically designed for this purpose, they are formulated to be "semi-drying" and designed not to shed pieces inside the motor if you get any excess squeeze-out (within reason, don't gob it on too thick).
mystic_1