You should be able to run the original iso through abgx360 and it will download the ss.bin assuming it's verified.
If you want to rebuild the folders after patching back to an iso then I don't know which app will do that as it's not something I've needed to do before. Does DVDMulleter do this? I've not looked at that app for ages.
Personally I use FreeStyle Dash and FTP to it and drop the extracted files in the relevant location. You don't need to worry about converting to a GOD. Unless you want to run it via NXE and not Freestyle of course
