[n4mwd]

Yes, #2 is on the right or clutch side, #1 is on the left or alternator side.

The EX line should be on the front and the IN line should be on the back.

If you have a timing light, you could use it to see if the flywheel sheered and slipped. The light should strobe when its close to TDC and you should be able to see the mark in the view hole. This is much easier than removing the cover.

In my experience with other engines, the flywheel can strip if the nut holding it isn't torqued enough. On the Ninja that is 50 ft-lbs. If you think you might have loosened the nut by turning it manually, this could be the problem.

But the valves are the first place to check.

I still think you should consider letting a pro take a look at it. You are rapidly running out of riding season up there.