So I tried the whole re-install the system and it said that the USB Windows 8.1 was not right, so I was not able to use it, though I don’t know why. They are both Windows 8.1 Professional 64 Bit installs.
I then tried the command line, but ‘sfc /scannow’ failed and wouldn’t work. So I did more googling and tried ‘bootrec /fixmbr’ to fix the Master Boot Record and it quickly said it succeeded. Still I restarted into Mac and made a Windows 8.1 install DVD in my Parallels install and set the restart disc to it, to try to use repair off of it, but amazingly when I restarted it restarted into my Bootcamp, which seems to be working fine now.
I plan on running Smart PC Care on it, but it isn’t starting now, so I am going to re-install it and run some utilities, just as soon as my NVIDIA GeForce Experience update finally manages to finish! Then I am installing my CalDigit drivers so I don’t kill BootCamp if I happen to have something installed in it. And then I am making a backup DVD so I can try and repair from that.
I am actually amazed that there are no Utilities to run from a second hard drive installed in your Windows PC to fix another install. I guess it is finicky about that, but I easily boot into my Parallels, so I could run a Utility on my BootCamp install, but am not allowed to.