2009 yz450f Top Dead Center Problem 2

Hello everyone I have a big concern regarding my 2009 yz450f. I just purchased this bike and was going to check the valves. When I went to get the flywheel marks to line up with the case mark They would not. I know for a fact the bike is at TDC by looking at the cam marks that align with the engine wall. I also put a long allen key in the sparkplug hole and when the cam marks aligned the key was at its highest. The flywheel/ left case marks are about 1 cm from where they should be. I took the flywheel off and I noticed that the woodruff key and crank all looked right. Could anyone tell me if their is a way that the previous owner improperly installed the crank? Also since the timing marks on the flywheel dont line up I believe my engine is getting false ignition readings. The bike does bog horribly when running and its not the jetting, I set the jetting to stock settings once I got the bike and the bike is stock. Could anyone send a picture of their 06-09 yz450f at TDC (the flywheel marks mostly). I would like to see if your marks look like mine or not. PLEASE HELP!!!

Is it possible that the crank bearing has play in it and is throwing off the TDC marks? I do notice a knocking when the bike runs even though im running 95+ octane gas. Could these marks not lining up throw off the ignition timing? Also the bike bogs and pops on decel. The jetting is stock and I just did the valve shims.

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