There must be another way than that though. While I can see it probably would work, it would be inconvenient to have to make sure I remember to turn the external drive on when it's time for backups. Which means changing their time run from the middle of the night to when I know I'd be around to monitor it, since I wouldn't want to leave on a enclosed drive 24/7 like I do my computers. Nor do I want the clutter of having an external drive.
There must be a way, or maybe a way to install Windows 7 without the EFI partition, I think that's the cause of the entire problem.
Edit: Actually I'm not sure the cloning process will work to a USB drive where it will be bootable. And if it did, I'm pretty sure I couldn't reclone from the external to the internal drive to fix the issue. If I have to take apart the computer to be swapping drives in and out, that defeats the purpose of how easy this setup makes recovery.