Did you replace or otherwise eliminate the failed hardware? It was not clear but that should be your first step, otherwise you are on shaking ground.
Yup - swapped all the drives from the bad chassis to a good chassis/motherboard.
Keep in mind that when a disk controller fails, it can pollute an otherwise working disk with corruption. Your own efforts at troubleshooting may have confirmed this. Your LiveCD works while your moved disks do not. I think you need to ascertain if any of your drives were corrupted by the failed controller and also remove that disk from the picture. You might consider using the LiveCD in the known good machine, placing a single disk into the system at a time and using the tools provided on the CD to examine each disk thoroughly.