John, when I swapped an 84 frame under my 87 El Camino, I was very fortunate that only the front passenger side body mount bushing hole was damaged. I attributed the rust damage due to the proximity of the drain of the AC/heater box which was right above. If not mistaken, I believe this location was #2. For my body style, there were a total of 7 positions along each side of the frame rail. It may very well be possible that GM used only 4 points for you sedan. The best way to check is get under and verify.
As for your reference to "ways to cross check these holes for square," I don't quite understand what exactly you are driving at. Are you referring to whether these body mount locations on either the frame and/or body are where they should be? If that is what you want to know, my suggestion is to have your vehicle inspected at a frame/body shop. Have them do an inspection by measuring specific points outlined in the field service manual. They do this inspection regularly when vehicles are in accidents. Do this BEFORE you do anything to your vehicle. If it is not straight, they can pull and align everything according to the factory measurements.
Hope this helps.