Your really over thinking this... mount the boxes where
they were before.... use some of the reference holes
in the unibody to make sure they are square to the car
then double check them to the axle... you should end
up with the axle square to the boxes AND the reference
holes..... if you look at the body you will see holes
in the unibody that line up on both sides of the car
these were jigging holes when the car was built