Hello mcquam, welcome to Seven Forums!
The thing to do is to disconnect the other Hard Disk Drive (HDD) and do at least 3 separate
startup repairs with system restarts between each repair
to finish creating the boot files to the Windows 7 C: partition; when finished power down the PC and reconnect the other HDD and all should be ok.
Have a look at this tutorial at the link below for some info; be sure to post back with any questions you may have and to keep us informed. Startup Repair - Run 3 Separate Times