I'd look the bike over for something simple. ..maybe a loose plug wire or maybe you hit the crank position sensor while removing or replacing the primary cover. Also you don't mention checking the free play in the chain. Good luck

 

Not sure what is causing the bike to run bad. Do you know which ECM you are using? Is it stock? Did you disconnect the battery during the work?

Also if you did not pull the clutch and comp off, you should go back in and look at the splines on the alternator rotor. They may be damaged.

 

 

 

Crank position sensor is right by your oil filter above the primary cover

 

 

Usually when compensator is loose on the older 10 spline cranks, the alternator rotor spline goes. It can actually get off center enough to drag magnets.

Also depending on how long it had been loose, the face wears (only thing driving it after spline goes is compensator spring and it still slips and spins)
That side wear lets sprocket move over and misaligns sprocket front to back.

Then it clicks at low full circle turn speed in a hard turn let's chain nip sprocket since most it can be off is 1/32".

Also, I have read how you torqued it. My experience is to use a torque wrench that is within torque spec. If you watch, 75 and then that 45 is mostly the compensator winding up. On your 05, I am not truely sure what you put on it. When I tried that, it was way low.

Also, need to make sure all that old loctite is out of that internal nut.

Just some thoughts. Your fix reminds me of my first one. What I am discribeing is my second fix to get it right.