When I made my model viewer I just copied the FF9.img file from the disk/Iso to my HD and it worked fine. As long as you're not reading the iso directly but just accessing that file through whatever utility can read an iso filesystem, once you open ff9.img you can assume a sector size of 2048 without problems.
Or ah, wait, are you talking about putting the data back on the iso. Then yeah, I dunno anything about that.