I'm completely baffled.
I had a look at both ends of the pedal mechanism and found no adjustment.
I'll check the pedal end again for brake sw keeping it from returning all the way.
My concern is if I do shim, shorten the rod, drill the mc and the problem 3mm disappears again while driving. I then have too little travel suddenly. Not that 3mm matters all that much.
MC piston punch thru was a concern as well. Not sure how thick the metal is on the piston.
I wish I had a good picture of the inner works of the booster. Might give some insight to what has happened if its booster related.
Very strange.

I did drive the car prior to parking it a yr ago. It had, what I thought at the time, bad brake hoses and loose tie rod ends. Its showing 156K miles and starts and runs as though the milage is correct. No rust Tx car.
The PO botched up the climate control system. I "manualized" the CC system while the car was parked and recently started restoring the front end and brakes.

The booster output rod seems to be captive but loose. I don't see a way to remove it. Perhaps I can make the change on the other end. It would mess up the ball end if I were to grind the rod.
I still want to find the problem before I sort to this.
Have another look tomorrow.