Nice work. Just a few tips/corrections...
As I understand it, the old, "unfixed" flasher does not work AT ALL, with any drives, old or new.
Both of the 5V lines, both of the 12V lines, and all three of the ground lines should be connected up. The cheap, crappy yellow (or brown) wires cannot carry enough current singly so multiple wires are required. Without them the drive may not be able to draw enough current to operate properly (have you noticed any of your wires getting warm? This is why).
Finally, you can cut away the protruding parts at the front of the drive to get the tray to sit flush with the front of the Xbox. That little piece of circuit board that sticks out doesn't have any circuitry that we're using anymore and the metal tabs that form the front part of the case are only there for the PC face plate.