OK, the above procedures for aligning the top and bottom graphics worked with the Skyboxes I'd ripped out of games up to that point. However, I just got through ripping a bunch of skies from a few different games. It seems that how the sky and walls of a skybox are aligned are not particularly standardised across different games - or even across different levels in the same game.

So, something a little more definite than the above is required.
The following seems to reliably get a ripped skybox ceiling and floor to align properly in GZDoom.
The skytopGet your North image and check that it aligns properly with the skytop by pasting the skytop at the top of the North image. You may find a bit of rotating and reversing are required. Once you know the correct orientation, mirror the skytop image (Ctrl-M in PSP) and then rotate it (Ctrl-R in PSP) by 180 degrees.
The SkybottomThis is easier. Align the skybottom to the bottom of the North image (rotating and mirroring as required). Once you have the correct orientation, save your skybottom image at that orientation.