What does the rod between the foot lever and the shaft on the engine look like?  The folks that like to stomp on the shift lever often bend this shaft.

What happens when you readjust the lever?

Pull the rod and check and check male and female threads?

I'll check once I get home today and attempt to adjust. I wasn't stomping the shifter, just a normal routine downshift at walking speed. Only unusual stress on the bike was getting stuck in stop and crawl traffic for an hour along the way. Oil level dropped a little bit. Otherwise can't see what would have caused this...

Ok it is fixed now.
When I thought the linkage and adjustment nuts were tight I didn't realize the front lock nut was all the way toward the back of the threaded part of the rod. It was tight to the end of the threads there and not up against the clevis where it belonged.

As for the mystery of how it got there I'm not real sure yet. Or why it seemed to happen really suddenly. I'm guessing it was gradual and I just didn't notice because after the traffic jam on my way home I didn't have to shift down to 1st for a long time.

I got a clue as to the reason it happened. Vibration!
I found a few loose nuts and bolts on my cylinder head. Since the big bore was done the motor vibrates a lot more at idle than it used to. And sitting in traffic so long things started loosening up. Then when I got out of traffic and the rest of the trip was at high speeds those loosened fasteners started really moving. So much so that one fell out and was stuck in the spark plug recess in the head. I'm still trying to figure out where that one came from, I ran out of light before I did.

Anyway's that's my theory. From now on I will make sure to snug up nuts and bolts before riding long distances or into possible traffic jam territory.
I readjusted the shift linkage and added oil. The bike seems fine now. Had me scratching my head though since I didn't have time to inspect it thoroughly before.