I fixed it in the end by converting my disk to GPT and writing a new EFI partition, which in the end means I can boot from UEFI which is nice. I do however have a new issue: I'm missing the Windows Recovery Environment. F:\EFI\Microsoft\Recovery is empty except for a BCD store, which has no entries. C:\Recovery is empty and C:\Windows\System32\Recovery is too. How can I fix this?