Rear caliper

[limax2]

The disc should be in the middle of the calliper slot. It is fixed by the calliper to carrier bracket fitting face, carrier to wheel spacer face, spacer to bearing, and position of bearing in hub. It is hard to see how any of these have become out of spec but I would start by checking the fitting faces of the calliper and carrier and correct length of spacer. If the wheel bearing on the disc side was not fully pushed in it would throw the disc to the left, but I think the bearing would soon have collapsed if that was the case. A longer spacer would also have the same effect.
Have you checked if the gap is the same front to back. i.e. is the calliper parallel to the disc in the line of travel.
I can't see how wheel alignment would effect the position of the disc relative to the calliper.