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2006 yz250f Misaligned FLYWHEEL!

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So im posting this in continuation to another thread. I recently rebuilt my motor again this year and ran into some backfiring after initial start up. I was confident the timing was correct. I also knew it was not the carb since days ago the bike was running fine and the carb was only removed and not tinkered with at all other then removal. What happened was the keyway on the flywheel did not entirely line up with the woodruff key on the crankshaft. Is somehow got a hair of and the proof of this is that the keyway is chewed up in the flywheel just a tad off from where the actual keyway is. The woodruff key is also peened over a bit. I just want to let people know what I ran into bc Ive done top end before and never had a problem but this was an easy mistake. Also I wanted to see if anyone could verify my theory that the flywheel being off just a hair would cause the backfiring through the exhaust since this controls the spark...or at least thats my logic.

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