First of all, my sincere apologies for not reporting back here in a more timely manner. Real life does have its complications...
So, this is what happened: I disconnected all drives, with the exception of my system drive, and attempted to boot the system. Windows refused to even consider that possibility. I then reconnected my drives, one at a time, trying to boot the system with each new reconnect. In the end, when I had all drives reconnected, Windows would still not start. I tried Startup Repair, which failed. I tried a system restore, but Windows informed me that there were no restore points to restore from. (Windows lies - I set restore points frequently). I finally decided that since I don't store any data whatsoever on my system drive, I would go ahead and do a fresh install of Windows. For safety's sake, I moved all data from my internal storage drives to my external drive using an Ubuntu disk. I then did a clean install of Windows on a larger (1TB) drive, and brought all of my data files back to the internal drives.
I attempted, while still in the Linux shell, to delete the bootmgr files that had mysteriously appeared in strange places. According to Ubuntu, they were gone; however, Windows showed a locked file on two of my drives that Windows would not let me get rid of - Windows refused to even let me go near taking ownership of those files. They appeared to be the Ubuntu version of the recycle bin. At any rate, I was forced to reformat those drives in order to get rid of the files.
I'm happy to report that while the whole process was a royal pain in my behind, I now have a clean Windows install, and all of my drives are at the point they should be at. I do have another question, but it's unrelated to this topic, so I'll post it in the appropriate forum.
Thanks for all of your help - I truly don't know what I would do without this site.