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Are there any tips concerning the use of 40+ year old transformers? Certainly, if the end bells are rusty they can be removed easily enough for stripping and painting (or powder coating).

What about the laminations themselves? If there is any slight rust on the edges, is it best to try to remove the rust or just leave it alone? If you try to clean it up, what's the best way to go about it?

I've noticed in some cases that the laminations aren't perfectly "squared". Part of the set has shifted maybe 1/32". Does this make any difference? Should I try to loosen the hardware, square them up, and re-tighten everything?

Wire brush, Ty, either hand powered or rotary. If using the latter, go gently; all you want to do is to remove the crud.

As far as trying to realign the laminations, fuggedaboudit. They're going to be just fine in their present form. You have to go 'way back to find transformers that would benefit from lamination adjustment.