Well, its done! The whole goal of this one was to return it to retail, or as close as I could get it. I probably went about building the drive the hard way, but what I ended up doing was using xboxhdm to build a new drive. In the xboxhdm\linux\C: folder, all I put in was a version of UnleashX with Ndure, renamed as xboxdash.xbe. Once I booted it up and had UnleashX running, I backed up the eeprom and then locked the hard drive. I then FTPed in and copied the eeprom.bin file to my PC (just in case), deleted UnleashX from the C: and FTPed a fresh copy of the retail C: in. I think the whole process probably took 30 minutes including burning the xboxhdm CD.
I cold booted it a couple times with the eject button and it loads up like any other retail box out there. Tomorrow, Ill remove the chip so I can use it in another project.
Thanks again for everyones help with this!