Do the HDD's have drive letters?
If not, can you assign them?
Try this:
FIXMBR
fixmbr device name
Use this command to repair the MBR of the boot partition. In the command syntax, device name is an optional device name that specifies the device that requires a new MBR. Use this command if a virus has damaged the MBR and Windows cannot start.
Warning This command can damage your partition tables if a virus is present or if a hardware problem exists. If you use this command, you may create inaccessible partitions. We recommend that you run antivirus software before you use this command.
You can obtain the device name from the output of the map command. If you do not specify a device name, the MBR of the boot device is repaired, for example:
fixmbr deviceharddisk2
If the fixmbr command detects an invalid or non-standard partition table signature, fixmbr command prompts you for permission before rewriting the MBR. The fixmbr command is supported only on x86-based computers.
You might have to flash your BIOS to support the drives.
Force the SATA drives in SATA 150 (GEN 1) mode for compatibility, on WD's I think it's jumper 5 + 6.
See if you can run CHKDSK on the drive somehow to repair the MFT.
If nothing else, a program by "EaseUs" called DataRecoveryWizard claims to be able to repair "RAW" drives.
If it turns out to be MBR or MFT corruption, which it porbably will, NTFS stores a backup copy or both so they can be repaired. MBR is harder to recover then MFT though, MFT keeps an exact mirror copy of itself.
You CAN do this manually with a sector reader/writer like DiskProbe from Microsoft. You can also change between Basic and Dynamic disk formats by doing this. (01C0, 3rd bit, 07 is basic, 42 or 43 I think is Dynamic, if I recall.)
Use NTFSInfo from SysInternals.com to find your MFT manually. MBR and backup are always in the same place, I forget where though.. GOOGLE IT!