Timing Issue?

I’m starting to get a bit nervous about the state of my 2012 Sportsman 500 HO (1500 miles approx. 150 hrs). Last night, i went for a ride and found a mud hole (mostly water) and i didn’t know how deep it was so I eased into it and slowly worked my way across. The water only came up just over the running boards. I got hung up on the opposite side and rather than hammer on it, I just grabbed the winch and pulled myself out. Pulled over to the side and turned it off to wait for my buddy to come through. Once he crossed, i went to fire it back up to continue on, and it would not start. Turns over fine but will not fire. Got towed out and picked up and today I started digging. First, I checked for spark. Got that. Then I checked for fuel, got that too. Then i checked the resistance of the ignition coil, and the pulse coil, both check out just fine (makes sense because its got spark). At this point the battery was getting low, so i put it on the charger until completely charged. Still won’t start (still turns over fine). I should mention that a few times while trying to start it, it backfired out the exhaust.

Continuing on… I decided to check if the flywheel had sheared the key off. It doesn’t appear like that happened. Everything in there is tight. I figured since I had gone this far, might as well check the valve clearance. Here’s where I’ve found a potential issue. When attempting to set TDC it seems that either the flywheel is lined up, or the cam gear, but not both at the same time.

First picture attached: Timing mark on the flywheel is lined up with the sight hole in the recoil cover. Cam gear is in the position shown.

Second picture attached: Cam gear is lined up as shown in the manual, on centerline with the crankshaft, and the timing mark on the flywheel lines up with the top bolt on the water pump!

I rotated the engine around probably a dozen times or better and each time, this is what happened. My only assumption is that something slipped when attempting to start it and the result is this. The timing chain seems like it’s tight and it doesn’t seem like it skipped a tooth (or several) but I can’t figure this out. Please help!

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