There are two areas I'd be concerned about if 1/4" of shims was used everywhere. One, the bumpers will be low. Two, if you have a steering box, you're going to have column to steering box misalignment.

I don't know why you wouldn't want to use the square shims that are sold to be used with the replacement body mounts.

If it was my car, I'd just drop the body on without shims, then inspect for obvious gaps at every mount, and add shims where there were gaps. If you started with shims, intending on removing shims either side of where you saw a gap, I just think you'd be chasing around and doing more fiddling with shims than the other way for no advantage. Once you have the gaps that you eyeballed shimmed up, you can start torquing the bolts, obverving whether some locations tighten more quickly or less quickly than others, and watching the door gaps. You may have to do some addition adding or removing shims at that point.