Please post back a screenshot of your maximized
full Disk Management drive map with listings, with all drives attached. Use Snipping Tool in Start Menu.
If you wrote the MBR to the new clone you should be able to boot either via the BIOS boot order or BIOS Boot Menu key. Test this.
Bootsect and bootrec are automated in Windows 7 Startup Repair. If either Windows 7 is not marked System now, mark it Active and run Startup Repair x3 while the other drives are unplugged. Startup Repair - Run 3 Separate Times Partition - Mark as Active
If you have any questions or are unsure wait until we read the screenshot. There may be other complications which will become clear once we see it. Going surfing til 7 pm PST.