Hi
Your hard drives should all be on the SATA2 ports. Do not use the Marvell 9128 ports for fast drives only for optical is safest. I believe that the ports you should use are coloured blue but they are the top ports.
I can only guiess at the other problem. You obviously have one or more devices that are not found. You will need to go through all the components that you have and see what is missing.