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That's a really good idea. A properly set up primary allows for a sweeter Commando.

Starting with the gear box, observe the main shaft alignment parallel with the crank. There's movement there.

On to the inner cover, you'll find a little movement in the placement of the screws.

I try to align the cover to center on the mounting stud. Set shims or gaskets as necessary for flush fit.

So on and so on...

Edit..you must posted while I was typing. Yes, straighten that up and things get better.