Perhaps better termed as checking for alignment and symmetry but "square" seems a perfectly good layman's term for it to me. It's interesting to see how they do that stuff for aircraft with datum plates, leveling jacks, floor marks, and a buttload of plumb bobs all over the place.
I did much like what Woodchuck says with my '67 once. The front was nicely lined up with good fender gaps and such but the radiator support was rotten due to a burst battery. I needed to replace it and some frame rail but wanted to keep everything in line. I took all sorts of measurements, diagonal and otherwise. I had pencil marks and notations all over the place. Turned out I didn't need 90% of those measurements were useless but the ones I did use were critical. One was a completely useless measurement from the shock tower to the bumper bracket bolt. But by checking it I found my frame rail piece had the bumper bolt holes incorrectly spaced back form the tip of the frame rail. It was easily corrected but I would have been sick if I had welded it all up then discovered it. It happens all my fender gaps and such went back identically and pleased my eye.
I have fastback quarters on my to-do list. I'd like to do some reference marking on those but that end of the car sure doesn't lend itself to the same style of marking up. I haven't really focused on it yet though. I was hoping to see a tip or two in this thread though. I'm actually considering doing a few aircraft style plumb bob references. Symmetry is kinda important to me. OK, well, sort of. It's really more like I'd rather not have people like Pete walk by my car and say stuff like "Hey, you know your quarter is crooked?"
