In order for the softmodded box to boot at all the hard disk must have a working C drive (at least to an extent, it needs to work enough to boot off a disc), and it must be locked. So you won't be able to use Slayer's at all until the HD is set up and locked with XboxHDM. Just get the EEPROM off the hard drive that does boot, a stock C off the Slayer's disk, and build a new setup using XboxHDM, then use a gamesave exploit / autoinstaller package (preferably Krayzie's NDURE installer) to mod. Alternatively you could probably use Kingroach's NDURE installer for the PC to set up an XboxHDM disk if you don't have an exploitable game.
In any case...the best thing to do is just get the EEPROM off your working disk and leave it alone after that (don't want to mess it up anymore since you're not going to be using it anyway, better to keep it as a backup).