Look at the LBA of the files you want to import. If you're lucky there are groups which will allow you to speed up the process by manually overwriting files in the hex editor. For example if you find 10 files that are in a row, open the hex editor, paste the modded files in the correct order, copy the whole file and paste it in the iso. In order to find the beginning just let the hex editor search for the first bunch of bytes of the first file in the group. Also make sure you fix the filesize by padding zeroes if your files should be smaller.
Also cdprog is basically much faster than mage. It does not update the TOC so will cause problems with programs like Makou Reactor but apart from that I'd recommend it much more.