To answer my own question (which is becoming a habit at this forum): http://www.sevenforums.com/tutorials/20864-mbr-restore-windows-7-master-boot-record.html
Turns out the Windows 7 Sytem Repair CD that I had made was the right tool for the job but I just didn't know how to use it. The link above explains how to use the command prompt window to fix the boot record.
The other advice I got was to have used the "Startup Repair" option at the recovery tools menu after running the repair CD but then running it three times. For some reason it needs three times to run before it might fix the problem. I think the command prompt window method is probably more reliable.