Is there a version of FatXplorer that sees the games drive? I imagine if he has them installed on E it would be ok, but all the fatxplorer versions I've seen don't see F & G. I think you're onto something copying C & E to the already setup drive though. Should be the easiest way. Copy C & E for a softmod to the drive and lock it, pop it into the 1.6, no?
Use a raspberry pi to grab the eeprom using PiPROM. It's just 3 wires connected to the LPC on the board. I had a unit with a bad hard drive. Well it would boot to the dash but freeze when trying to load a game or anything. It was weird. Completely untouched system. PiPROM saved my 1.1v xbox. From there I was able to lock a hard drive with the xbox hdm usb 2.3 and install to the console. It took me a few times because I pulled a corrupt eeprom and wrote it to 3 different drives.
Long story short, read eeprom and open it in live info to make sure it is not corrupt prior to locking a disk with a bunk eeprom.