Kev,
You say that the engine and gearbox are separated, and that the clutch is out. By that, do you mean that you have undone the 6 5/16" nuts around the flywheel and removed the pressure plate and friction plate? If this is the case, check to see if you have any free movement on the clutch operating arm - if you have, then something is preventing the 6 bronze bushes from sliding freely through the flywheel. At this stage, you could try loosely replacing the pressure plate, and using a large screwdriver, try levering the pressure plate away from the flywheel (as would happen when you lift the clutch). You will find an alignment mark on the O.D. of the pressure plate (the flywheel and spring plate have similar marks - they should be aligned on reassembly). Having tried levering the pressure plate away from the flywheel, dummy rig the cable and handlebar lever to check that the clutch will lift as intended - this will overcome having to remove the flywheel (as you have found, they can be extremely stubborn - and the extractor holes are hardly man enough for the job). I usually resort to undoing the flywheel nut a couple of turns, loading up the extractor, leave it for twelve hours or so, then give the nut a sharp whack using a soft drift to prevent damage (dont overdo the whacks, as that can send the crank forward in the cases!).
Hope some of this helps,
Regards,
Eddie.