Thanks Klarth, I wasn't aware of the 64MB window. Presuming I'm smart enough to get the command line utility working (checking into the documentation on xdelta.org right now), I have two concerns:
1. It looks like my life might become easier if I kick up that default window to, say, half a gigabyte (Dragon Force II is 570MB all told). Anyone know if a value that high has ever been used, or does this sound absurd? There's a single file in the game that's 300MB in and of itself, so it really throws the whole image out of whack if it's misaligned between comparison copies.
2. If I use the command line utility to create an XDelta patch, does the end user have to use the command line utility to patch too, or will front-ends still be compatible with a patch made with a wider default window?
I'll check around for other XDelta front-ends too, but I have a feeling SadNESCity's and KaioShin's are the best available currently.
Barring these considerations, I suppose what I'm looking for is some way of building a CD where I can copy the file order from Sega's original print and use that as a template for ordering files in the translated build. I've been using UltraISO to build my disc images from the file set, and try as I might I'm not seeing that sort of option.