Update: I re-flashed the backup to it through raw block copy, now it detects nothing, not even in the alt menu.
Now the system wont even boot ANY cd's, Tiger or OS9.
Still boots to Tiger from the hard disk though... when I swap it out.
I'm starting to worry its the optical disk at fault for one reason or another.
Edit: Aparently my Superdrive is a picky disk eater, dug out some older CD-R's and I am booting into the OS 9.2.2 Install. Progress is being made!
Edit 2 : Fixed, just had to load startup disk through install disk, feel free to close!