Rotor does indeed have to remove, the crankcase there goes slightly inside the rotor where it has a recess on the back of it. On all early DOHC except possibly the 1100 because that rotor is different and narrower back there. The smaller engines need the extra flywheel weight of the thicker part.
Dangerous to remove rotor with cases loose, the violence of it may do case-to-case damage. If I were you I would bolt them back up solid, not to torque and not all bolts, just enough to firmly hold the cases together. Say crankshaft area bolts for the mains.
A rear axle to rear wheel makes an excellent puller.