i just had fun, ALL my raid cards died today, then the onboard bios wouldn;t detect all my CD's, after i got the raid cards to work again (Minus1) the bios wouldn't boot from cd so i could re-install windows (Was in process of upgrading all systems)
in end, i stripped every pc, pluged in one peice of hardware at a time, even did some cable management while i was at it.
PS, let us know the outcome of your tests getting HDD's to work, it might help someone else in the future.