Removing lower crankcase - KZ550

I need to replace my transmission output shaft. Is it possible to turn the engine upside down and lift out the crankcase bottom without removing the clutch or loosening the clutch nut, without removing the sump and oil pump,and without removing the secondary clutch and starter clutch?

No is the long and short answer.
To split the cases, the secondary shaft and starter clutch HAVE to come out. To get those out you have to remove the clutch in its entirety and the oil pump.
The crank, rods, pistons, cylinder block and head can stay in place.

Awesome - thanks. I haven't lifted a finger to do anything yet, I'm just getting my head around what I need to do, and plan the operation. I'm also buying the relevant gaskets and seals.

One more question: to rejoin the 2 crankcase halves, would Hylomar Blue (non-setting jointing compound) be sufficient, or would a copper-based gasket-making compound be more suitable? The workshop manual says to put "sealant" almost all the way around the mating surfaces, but it doesn't say what type.

Use Kawabond, Hondabond, or Yamabond non-hardning sealant to seal the cases. Use a thin layer. Do NOT goop it on.
Get a manual for your bike and read it 2-3 times before you attempt what you are attempting.

Good luck and have fun!