I'm starting to think it's an - 03. I've just opened The Magical Box of Motor Mystery and discovered the other, original, "rebuilt" motor is a 12 finned (well, 11 - what is it with me and dodgy flywheels?) 1500Z type.
I also discovered the reason for cut down bolts on the handle bar anchor adjustment points. The later carb with snorkel doesn't seem to fit with the earlier setup as there isn't enough clearance between the filter and the bolt head.
Still can't figure out why I'm getting contact with the flywheel on the later engine. I've also now popped the filter housing back on and she won't start. Ran out of daylight, so that is a problem for next time.