The first thing to do if you haven't already is to back up the EEPROM.Bin file and FTP it to the PC. With that you can re-lock the HD if something were to go wrong.
I gather you are still working on the larger HD. If I were to restore an Xbox to stock, it would be the original HD. A quick note for future modding projects. I run the exploit, Krazie's Ndure 1.1.1 and go to the back up eeprom selection. From there I stop and FTP the C and E drives to the PC. Then I take those files and use Xboxhdm to build a new drive. Put that stock drive in the Xbox and run the exploit again and fully softmod it. If anything goes wrong, I can still put the original drive in it and have a stock Xbox with the only modification to it being a back up of the eeprom on the E drive.
FTP into the Xbox. Delete all files on the C drive and FTP the C contents from Slayer's to it. That should restore the MS Dash. While in there you can delete the files on the E drive and that will get rid of all game saves. When you reboot the Xbox will rebuild the TDATA and UDATA folders.
If you still want to try to save the modded Xbox you could try CASH Ver 1.1 or Frosty's rescue disk.
I don't know why Slayer's wouldn't restore the HD to stock. I have only used that option once or twice, but it worked.
Good Luck.