I'm pretty late on updating this, but I found the issue.....and I was correct about it being a timing problem, although it was ignition and not the valvetrain.
Although you couldn't tell by looking from the outside, the case cover (magneto side) has busted the wall between the sprocket and magneto. That let mud and pebbles get into the flywheel area and a pebble must have wedged between the flywheel and pulse sensor, causing it to break.
Unfortunately the pulse sensor is part of the entire stator assembly, so I have to buy a new stator, flywheel puller, and case cover with gasket. But it's all good......I had been wanting to add a light to it anyway, so this gives me all the reason I was needing to upgrade to the 110 watt stator from Baja Designs......which is still a lot cheaper than the OEM stator.
After all is said and done, I'll only have less than $175 in the repair......and that includes adding the light.