What you should do is get an XBOX bootdisk. These can be made quite easy. You can either choose to burn a CDROM (use a CDRW for best reading capability) with a desktop like EvolutionX on it, or to get a standard XBOX bootdisk. I kinda like Slayers EvoX installer disk (there are some good others btw). These all-in-one bootdisks allow reinstalling an XBOX harddrive and will restore the boot capability. Just remember that you need a mod to make this work, so I hope your mod is working fine.
Oh and before you format your XBOX harddrive, be sure to backup the folders "UDATA" and "TDATA" on drive E:, as all your savegames etc are there!