I finally fixed this issue. I tried repairing my Windows installation but none of the options let me do what I needed to do, which was to reconstruct the boot manager on C: drive.
After some more searching I found a forum thread with this exact issue and a simple solution. Well, simple in execution but I had never seen it before. I will quote the solution:
You can open an Administrative command prompt and type the command below to place boot files in the C partition. Make sure and put spaces where indicated or copy and paste the commands.
bcdboot c:\windows /s c:
Then shut your system down and disconnect the other drive. During reboot, make sure drive 0 is set as the primary boot device. The system should now boot normally but you may not have recovery options available. So before you shut the system down you might run the command below in case you need the info, it should show the path to the recovery tools so save the listing.
I did what was posted and WHAM it worked. Once I had rebooted a couple of times without the other drives connected I went ahead and shut down and replaced the drive that had the old boot manager on it as it had been causing me some problems, as well as replacing my SATA cables with some black latching ones.
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