"My governor was out of time. Is there a possibility that something else is out of time?"
YES, most likey simply the mag versus all that other stuff. Again, Flywheels LHI at 3 o clock by mark,,,,,,Left piston at TDC,,,,,,,Open female slot in governor shaft end (where mag mates) horizontal fore n aft,,,,,,,,,Adjust mag so it snaps/impulses exactly then,,,,,,,Forward CW retards, backwards CCW advances.
"I am rotating the flywheel around (CCW facing the flywheel - I hope that is correct)."
"The mag seems to impulse just before I can get the marks lined up, or possibly right when they are lined up-its hard to tell)"
If it snaps impulses BEFORE then it needs retarded, losen and rotate forward CW. Ideally you may have to go at mags rear and adjust the lag angle to accomplish that if the above dont get it there. That adjusts ONLY the lag angle and snap impulse timing NOT run timing
"I had my mag just rebuilt by a professional. From what you are telling me, there could be an adjustment that needs to made to the mag."
It may well need the rear lag angle adjusted, perhaps nothing more, its not serious, just needs some attention. As I stated when all was new and perfect and lag angle set correct the snap would occur right when the mag is straight up n down in the middle of that adjustment window.