I tried to gently tap the rod back just on the off chance it would pop back to the correct position. No such luck.
I don't see any evidence of anything bent or damage. It is a mystery how this came to be.
I may make a shim for a temporary fix until I can research this a bit more.
I'll need to maintain the seal for the booster though.
Or, I even thought of drilling the MC about 3mm deeper. Either way, it will be a "patch".

I think I'll adjust the valves. I could use a 'break'.