Mybe no help to you, but: You DID get a boot sound normally? My cube doesn't make any noise (speaker-wiese) on startup. I thought since the usb speakers need to be powered and have their system driver loaded, that's the explanation for no boot sound.
For your problem: The RAM sounds promising, true. had horribly problems once because of faulty RAM. was there any point in time when you put something new in ths system or changed something that started it all off?
Since the symptoms are changing all the time and you get nowhere with the hardware tools cd, have you tried an apple dealer? seems like you already put quite some money into the quest to find the culprit (new HD, new motherboard), so why not try the guys who should know?