Timing--- Crank---Cam--valves

2007 Powler XT 650h1 is what I have. I have no regrets I bought it cheap...and seller told me they could not get it started. What I was told was they took it out, went through a major mud puddle...and it died and would not start up to run again. Well, after I washed all the mud off the motor, inside cab, outside cab...two days later I could actually see what was underneath all that mud! Important note: while I was looking around, checking for spark and wire, computer connections...I did notice permeant marker marks on the top end as someone had taken it apart some time ago..perhaps to change the Cam chain? but..I figured they did a good job cuz it ran and got mud all over it...but due to the blow back I was getting at the carb...and the erratic way it was sparking at the plug ... , I went back in my head with all the small engine stuff I had gotten into...and my first thought was a sheered flywheel key. But that was on small engines with weak keys...I wouldn't think they'd use a weak key for a beast motor like this...so I watched a video of a guy checking the top end Cam chain and timing! What the hell...someone in the past was in there doing what? all them red permeant marker marks. Well...I took the top end off...before that I opened the eye hole for the timing at the crank(flywheel) lined up the line at TDC all valves closed....then I take top cover off and look at the Cam timing...it should be left to right edge of casting as a guide...well....IT WAS NOT...it was more UP and DOWN...I'm checking this out and there's no way that I can see this new looking chain to have jumped that much! So?? back to my old thought?? Key is sheared and flywheel is stuck in funny spot? or.......piston rod is slipping on the crank?? Am I missing something some thing here? I have a stupid question too...on small engines...if I was turning the flywheel by hand and I went past where I wanted it to be...I could just reverse my rotation with my hand a little and get it where I wanted it...On this thing.....I can only rotate it in one direction!!????????? Thinking out loud with ya folks here...so any thoughts or idea's to all this...what could I be missing or should check? I have NOT taken the cover off yet to see the flywheel...as it will envolve undoing the water pump too and the clutch arm.