There's probably no keyway on a mini rotor. And yes, this is why your bike runs like shit. If I had to bet, the flywheel is cocked and only holding on one side because it's taper is different. And even if the taper is the same, it might not sit far enough back on the crankshaft to induce the needed current in the coils. Also do they rotate the same direction?
Ignition swapping is possible, but not without a lotta picky attention to detail and likely some pretty involved machining