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Ignition Module is $250. I think I'd pull the valve covers first and check there. If the module is bad it should affect both cylinders. Single or Dual fire ignition.
If you decide it is ignition don't forget the trigger in the nose cone. Could just be a loose bolt.
Removed the front valve cover to check the springs. I can't tell if there is a broken spring. I also watched the springs while turning the bike over, the only things that I noticed is the front rocker arm would move a few times before the rear one would (2-4 times) before the rear rocker arm on the same cylinder. Also the front spring did not seem as stiff as the rear when moving.
I also noticed but not sure if its suppose to be like this, the pushrods seem to be riding on the walls of the pushrod sleeve
Both rocker arms should move an equal number of times per cylinder. It takes an intake and an exhaust to make the engine run. I think you may have missed a few when you were watching.
When I was watching the rocker arms, I just turned engine over, and it looked as the front rocker would move twice before the rear would move.
Should I actually let the engine run and then watch them?
No; Do not start it. Just turn it over in the direction it runs. The exhaust valve should open first, then the intake valve right after the exhaust. There may be some overlap where the exhaust is just closing, and the intake just opening. The valves should do this every two revolutions of the crank. If it is not doing it this way, you either have a stuck valve, or there is something wrong in the cam chest.
Removed the front valve cover to check the springs. I can't tell if there is a broken spring. I also watched the springs while turning the bike over, the only things that I noticed is the front rocker arm would move a few times before the rear one would (2-4 times) before the rear rocker arm on the same cylinder. Also the front spring did not seem as stiff as the rear when moving.
I also noticed but not sure if its suppose to be like this, the pushrods seem to be riding on the walls of the pushrod sleeve
I'm guessing you are using the starter to turn it over slowly by bumping the button? If so, when the rear cylinder is on the compression stroke and you bump the button but it doesn't pass the compression stroke, the compression would push the engine backwards when you let off the button, opening the intake valve on the front cylinder back up. As far as your noise, I'd pull the lifters if I were you. You already have the pushrod tubes off, it won't take much. Just check the rollers on the bottom for up and down movement, there shouldn't really be any. If I had to venture a guess, i'd say one of them is worn and it's acting like the valves are set loose because of the wear. You would likely hear it in the top of the engine, because when the valve closes and the tension comes off of the pushrod, gravity and inertia pull it down with the lifter, and when the valve begins to open, the clanging you hear is the pushrod hitting the rocker arm as the gap is closed up again.
The Scoot is Fixed. The issue was actually the lifter, the bearing was shot, and had alot of play in it. Replaced the lifter, and seals, put on about 100 miles and all seems good.
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