I’m not an expert yet, i have got my mil running, but if you want my $0.02
Re: 4b: can you just move more of the pipe through the corner pieces? Send easier than printing more parts. You can leave spare belt at the end too, so you could have a 10″ x10″ build area without cutting anything.
Re the rest:
I would be interested to know if there was some repeatable way to push the bit laterally, and measure the deflection. Ideally something someone with a working mill could also do. That would eliminate any tool/milling issues. It might also be a good metric to test when making changes. You could also try measuring the movement of the roller assembly while the steppers were holding in place, to see how much flex there is in the belt. Sort of some subsystem tests to narrow it down from the system test.
The other thing I can think of is, is your bit sharp? Do you get problems milling foam?