Maybe the key that positions the flywheel on the crank has stripped.

 

Pull your flywheel. I bet the woodruff key is sheared. I have repaired a few of these bikes with sheared flywheel woodruff keys. Even had one break on a 1994 Kodiak 400 (essentially the same bike and engine, just bigger piston) I once owned.

FYI only.
Once you get that bike working good, don't ever get rid of it. They just do not build them like that anymore.
For a preventative maintenance measure, pull the rear axle and clean and grease the crown gear splines. These are known for stripping due to rust after about 10 years or so. Used axles are almost non-existing, and new ones are stupid expensive.

 

If the key was sheared or starting to then how would the the timing marks on the cam and flywheel line up?

 

The flywheel woodruff key has no effect on the timing marks. Only the timing chain effects that.
When the flywheel key shears, only the timing of the crankshaft to flywheel is effected. Since the flywheel is timed to the camshaft via a chain, these timing marks will still line up.

 

I agree but im 99% sure thats not the case because the timing marks are on the flywheel itself. When the cam mark is lined up the t mark on the flywheel is lined up. Whick is making me think its a electrical issue. Am i looking at it wrong?

 

You could be right on the the problem may be something else....but your thoughts on the timing marks is incorrect. The flywheel woodruff key has no effect on the timing marks lining up in the windows. All that key does is line up the flywheel in the correct position on the crank. You can line up the timing marks in the windows, then install the timing chain.....but if that key is sheared, you have no idea where the crank is positioned.

I have replaced a few of these sheared woodruff keys on these bikes. That's why I mention you should inspect it as it is a not-so-uncommon part to fail and give you the symptoms you got.

 

How would i check where the position of the crank is. are there more marks behind the flywheel? is there any tricks to pulling the flywheel with out a flywheel puller?