After setting it aside for a couple days, occasionally thinking on it, finally came back to it.
Found out what the issue was, and have fixed it. Everything working fine now.
Problem cause: While doing the initial editing to bring the ships into the mod, for the cruiser and capship I'd only made placeholder variants, single weapon, nothing else, via Trylobot's ship editor. After I'd gotten everything else working, I went back to those placeholder variants and used the same file, making proper, fully loaded variants, but somehow the variant file got farkled up. Looking at it, the initial placeholder weapon info, or parts of it, didn't get removed properly. So, while the game would look and see the variant file there on game startup, once it actually needed to read the file, it would crash.
Solution: Deleted original variant files, remade them from scratch, again with Trylobot's ship editor. Everything works fine now.