FF6: Messing with the final battle lineup

My most recent attempt had me restart at the Solitary Island and get the correct minimally required characters, then take them directly to Kefka's Tower. I saved outside, changed the party to three characters I hadn't recruited (Locke, Cyan, Relm) and they were immediately overwritten by the cutscene from the first time you enter the tower. So I went through that scene, saved again, and edited my three characters back into the party (all using $1850-$185F). They were again overwritten by the correct three once I entered the party selection screen.

So, I played through to the first save point I reached, just before Inferno, and tried it again, this time with Relm, Locke, and Gau; Gau was able to proceed from the save and fight Inferno but upon switching parties, Locke and Relm both appeared in the airship instead of in the tower, making the game unplayable. I am still not sure if this is reflective of the kind of breakage I should expect, or if I broke something more obviously.