Go into your bios and see what settings are under disk configuration - see if the hard disks are detected correctly - Im only guessing here, as I dont know enough about PCI IDE - I gather they arent sata drives is that correct? I would also say at a guess you might need to get instructions from the manual for the PCI card as it would have a driver
that needs to be installed maybe at the start of installation of Windows 7, if it asks whether you have a SCSI DEVICE and to press F6 - these drivers
have to installed to a bootable floppy disk prior to installing Windows 7. Im not sure Windows 7 is the same as the prior OS, but have noticed you can install a driver when you reach custom install, however, it may ask at the start of installation. What you need to do is post back the name of PCI card or do a search - Bing or Google, if you haven't a manual or something (an install cd) with instructions.
So you have attached the drives and restarted - OS wont boot - looks like your missing a driver - did you have the PCI Card attached when you first installed Windows 7? If you did there would have to of been an unknown device in device manager with no driver - if so you need to disconnect the drives, and install a driver, and then retry.
I'm not sure on this one but I think you should be able to resolve it.
*I just read the last bit of the reply which said you unplugged them - can you boot to Windows 7 with them unplugged, as you said you tried the repair option again, that doesnt necessarily mean you tried to boot to Windows 7.
If you cant get back into Windows 7 you might as well reinstall the OS - BUT make sure you have available drivers and correct bios settings and you should be able to find these with the install cd or motherboard manual. This bring s to mind - have you the latest bios installed?