does the gearbox need to be removed when splitting the crankcase?

Gearbox is inside the crankcases so you can't remove it without splitting them!

Actually, which bike is this?

sorry, its an NC30. I know the gearbox is inside the crankcase, but I was wondering whether the input/output shafts were in different halves of the crankcase's

The gearbox stays in the bottom half,Lift the top off.

I have removed all of the bolts that hold the two halved together (external, and the internal ones inside the sump), including the water pump, oil pump and starter motor. I gently tapped the outer edges with a rubber mallet. A slight gap has appeared between the two halves but will not separate any further. The Haynes manual says that you should also remove the gearchange mechanism, ignition pickups, clutch and flywheel. I am not that familiar with this engine, but other (two stroke) engines I have split in the past didn't require the removal of the flywheel as it simply hangs off the end of the crank. For anyone who is split these engines, it it really necessary to remove the clutch, flywheel and pickups?

Yer you have to get the flywheel off, as there are 2No bolts behind it holding the crankcase halves together.
You can (from memory keep the clutch on) but if you are going to teh extent of splitting the engine i would have it all apart and check everything better to do it now than when you have it all back together and realise you need to check something.

A Haynes manual would help you no end in this situation.

Highly recommended.

Clutch has to come off to get the oil pump chain off, and the input shaft bearing retainer. And yes the stator needs to come off, because it bolts to both halves of the case.

FYI - the crank, clutch and gearbox are in the top half