Cleaned, zoomed, lighted, cropped…I still can’t see no index mark.  I’m blind!

Blowing up both pics, the arms look the same. The rod however is closer to the case on the black bike. Most likly bent, or something modified on the front end.
Get down close and have someone else shift it. (engine off) It will be hitting the case. You should see marks in the paint on the case.
Take the whole assy off and look for a bent rod, and post a pic.

Arty,  You are looking at 2 different things here. Monkeying with the clutch adjustment is NOT going to fix a shifting issue. Once you are moving you should be able to shift up and down without touching the clutch lever, it won't be smooth, but the bike will do it. I have ridden 60 miles home with a broken clutch cable, had to come to a dead stop 3 times. Wasn't pretty, but I made it.
A shifting issue is a shifting issue,
A clutch issue is a clutch issue.
If you can start the bike pull in the clutch and put in gear, any gear, and hold the clutch in and the bike does not move, the clutch is disengaging.
If you let the clutch out and the bike moves, the clutch is engaging.
That is enough to tell you the clutch is good enough to ride the bike.
Not shifting is a different thing totaly. Either your linkage is messed up or,,,,,,, you have internal tranny issues, they make loud noises and poke holes in the cases.
I still think the shifting linkage rod is hitting the case.

So I put back the standard clutch pin, but the bike is still hard to shift. It's almost like it just skips 2-4 gear. I can hear a click on each gear, but the click is light and definately can't control it with my foot.

I've straightened the rod, but it seems to be still bending so I guess I need to replace that.