Navagon: I was able to 'fix problems with starting Windows' using the USB flash installer while the other drives were disconnected. This created the boot partition in the right place this time. Given that you were the most helpful I marked your post as the solution.
Thanks!
You're welcome, I did get a bit worried that I had been talking completely out of my arse after people corrected me a couple times. I mean, my posts not contributing to the discussion is par for the course in most cases, but I don't like to give false information which in the best case may just send people off on a track that just takes them further from a solution.