I'm not sure I understand how it could be out of time with the flywheel. Are you saying it doesn't retract all the way?

I was only curious if there can be a "timing" issue between the flywheel and pull cord. I'm getting the "cord trying to rip my arm off" after I pull it out about 2 feet by completely stopping. If I pull the s*it out of it, the engine will turn over. It is a Troy-bilt mower with a Honda engine.

The flywheel key is not the problem, I already checked it. When I disconnect the spark plug wire, tilt the mower back, and disengage the brake, I can get 2 revolutions with turning the blade by hand, but then I get two short spots with a lot of resistance. Then after those short spots, i can get 2 revolution, etc...same process repeats. I still get the same resistance when the spark plug wire is disconnected and I pull the pull cord like normal from behind the mower.

Could it be something in the engine?

How does it move with the spark plug removed?
Is the flywheel brake adjusted properly?
If you still have the problem, then it looks like you answered your own question.

Try putting the blade back on or double checking that the blade hub is locked to the shaft.

I removed the blade and cranked it to see if it was the blade, but no luck. with spark plug removed, still the same resistance when move the blade by hand. Yeah the brake is correct.

I had a lot of problems with the lawn mower. I found useful information herehttp://grassshackrecords.com/