Since the CD's audio track - a cute little message you get when you pop Dragon Force II (J) into a music CD player - appears to be the culprit, my first instinct is to have the user rip only the game data track to a .ISO file, and use that as the original image to patch. The hope is, if the user produces an image that excludes the audio track, the user and I can produce ISOs with identical checksums. I'm waiting on feedback from others who have Japanese CDs of Dragon Force II to test this idea. If that works, delta patching will still be viable for distributing the project; I just have to add some patches for that method and re-work the readme.
But if my Hail Mary pass doesn't work, I'm on the lookout for alternatives. I'm aware that the Shining Force III translation team made a custom patcher that basically rebuilds the Shining Force III ISOs from scratch, but I want to make sure I'm not overlooking non-custom solutions. The patching programs listed here at RHDN heavily favor delta patching; is anyone aware of tools that can patch a CD that conforms to the standard ISO format? Or inject files into the CD, over-writing the originals and adjusting the offset table to account for different file sizes?
Some insight on my current process: I use UltraISO to inject the English files into the original game image, but I've written this off as a viable method for distribution because I haven't found a way for that program to preserve a bootstrap loader that's necessary for emulators (and probably the Saturn itself) to read the disc. I have to manually add the bootstrap loader back in with a hex editor, and that result is what I use as the target image for the delta patch method.