You might wanna extract separate partition images from the ffu then edit the MainOS image but you can't repack them into a new ffu. You can only repack those images into a flashable zip file. If you're not in hurry, I can write a full tutorial next week if you need one. Otherwise, you can experiment yourself with Interop Tools, OSFMount and Total Commander. Just be very, very careful cause you might turn your device into a brick