Quick suggestion. I don't k now if you pay Microsoft (or whomever) for the fat file system licensing, but I have a suggestion. To avoid necessitating that, or stop the need to split iso's. I propose using the Linux file system ext4. There are freely available drivers for windows and OS X out there (which could be provided on your site).
Or maybe, the ISO manager could be the ext4 file system viewer AND firmware updater AND automatically do what's currently a custom job of having to create a config/isosel.bin and config/iso_filename.txt etc.
I'm also, essentially, willing to donate my time to writing the software required to make this as simple as possible.