Just some thoughts Martin.
Looks like front fork "A" (1st/4th) might be bent, and the wear is definitely not good. It for sure has to be responsible for your 4th gear shuddering, and at least some of the swarf found in the sump strainers.
You could measure the clearance between fork and the dogring groove with a feeler gauge each side, but ultimately I would replace the fork.
There is some wear on the detent wheel dogs, and the detent claw that turns it might be spread slightly - perhaps someone was kicking it through the gears a bit too heavily and caused this plus the (possibly) bent fork, causing the shuddering and difficulty shifting.
But the output shaft gears do seem a bit too wobbly, I wonder what the clearances are like in the components. 5th seems to move very freely, maybe too free, might be worth replacing the opposing bevelled washers between it and 1st while you're in there - this will probably improve your issue getting it into 5th at least.
Do you think all the swarf in the strainers came from that front fork?
Would be checking rest of engine while I have it apart. Plus opening the oil filter.
Yes the forks must be lined up where they normally operate, or shifting doesn't work right as you've found. Also a transmission will shift better when turning as I'm sure you've found.
Out of interest, I wonder are your circlips the right way round (they have a somewhat rounded edge on one side, and a sharp 90° edge on the other - the sharp edge goes outwards)
There is also the option of sending the trans to Bill Robinson in New York to give it the works wrt deeper & stronger circlips, and undercutting dogs. Maybe even the billet 4th output cog if you felt like it.
