Ok thanks to
@Luis A. I have procured China’s finest alignment tool. There are no instructions except for the cryptic ones on Amazon, and the text on the device is confusing, but the blind squirrel has adapted and overcome!
It doesn’t fit over the master cyl (as several in the reviews noted) so I whittled the edges down to clear. I used the rounded end of the rod to measure the distance inside the pipe:
View attachment 176856
Then put it on the booster to see the clearance with the rod (the tip pulls straight off the rod (does not unscrew)).
View attachment 176857
Even with all 3 washers off it was still barely touching so I sanded just enough off for .5mm clearance:
View attachment 176858
So basically the MC was being pushed in by at least 2.5mm over spec. It appears to me that the inside pipe of the MC bottoms out right at the front edge of the booster, so you want the tip of the booster rod to be just under the front edge. I’m hoping this solves the issue and provides insight to those replacing a rebuilt booster in the future. Onward.