Ok may be i missed something?
Is this correct?
1. You have 2 HDD both with the same Windows 7 image.
2. You can access either of those drives, but 2 x Boot Options (Win 7) are shown at the beginning?
If the answer is yes to both, access either, download EasyBCD and remove one of the boot installer version of Win 7. Restart and enter Windows 7, right click on Computer, Select Manage, Select Disk Management, Delete one of the Window 7 Partitions, and then Select both disks and create a RAID.
Only do this if you answer both Yes and you have a back up of your files etc.