You might do a little more homework before you go changing the subframe alignment. They are called alignment holes because they are areas that pry on/in to align the frame.
I'm not positive, but the alignmen of the holes as to how they relate to each other doesn't nessessarly mean that the frame is out of alignment.
I belive they call it the x-y measurements, and you do the aligment by measuring given points, not by aligning the holes.
Again, I'm not positive, but it seems that they wouldn't give alignemt specks if one simply aligned the aligment holes.
Here's a couple of pictures from my 69 service manual. By the way, the book says that to align the frame, check the measurements and adjust. But it says nothing about simply aligning the aligment holes as the way to align.
Heck yes it will foul up the adjustment of the sheetmetal.