Use Paragon Rescue CD to change back drive letters which slip during cloning or repair: Moving Win7 Partition to Another Drive
If you have any WD or Seagate HD's involved then you can use their free Acronis cloning apps which are the best. Find them on the support Downloads webpage for your WD/Seagate or we have links. Ifnnot, us free Macrium Reflect to save externally an image and reimage onto the target HD. Then boot via BIOS boot order or BIOS Boot Menu key which is the preferred method rather than interlocking HD's using Windows dual boot manager.
As I stated earlier all bootrec and bootsect commands are automated in Windows 7 Startup Repair so it is the random commands run which likely borked the OS.
Does an installation still appear to repair when you boot into Recovery console? If so, it should repair. If not, then it is sometimes useful to then run bootrec /fixboot and bootrec /fixmbr to goose them to be seen by Repair.