FWIW I experienced "Y" misalignment about 15 years ago with a NEW vertical mill ! The solution, as proposed by Tom in post #3, was to carefully shim the joint between head and column (my vertical mill is of similar construction to yours).
Personally, like those who rebuild old autos, I think that getting old iron up and running is part of the satisfaction of this hobby, LOL
Personally, like those who rebuild old autos, I think that getting old iron up and running is part of the satisfaction of this hobby, LOL