Nothing of that should actually have even a sliver of hope to work, as far as i can understand?
It's all read from the drive, after it boots. I think i have the same issue without fastATA & with a CF. A hot reboot always works for me while a cold boot never does. Any MapROM switches still needs the system to boot a first time, and consecutive hot-boots can be "fixed".
RetroFan, you tried coldbooting, look at the "InsertDisc" image for 5-15 seconds, and then doing a hot-boot?