how do I check that the flywheel is correct?
Remove the spark plugs. Put the bike into 3rd or 4th gear. Put a long straw in the open plug hole. Turn the rear wheel in the direction of forward motion. Watch the straw and the OT mark on the flywheel through the timing hole. Also watch the valve action at the same time. When the flywheel is at OT, the straw should have moved the furthest out that it can possibly move. You will also notice that both valves are firmly closed. If none of this matches up, then the flywheel has been installed wrong.
how likely is it that the magneto rotor moved?
Not that unlikely. If it wasn't secured to begin with. If the two tapers were not cleaned properly. If one or both tapers were damaged in some way. Could be that it's just been this way for some time.