The Windows installer isn't the brightest regarding installing things that would make sense to a person.
The simplest method would be backup data, disconnect all drives but the intended one for the operating system and reinstall.
The harder approach and much more technical (and there is risk in bricking the OS anyways)
- From a different OS such as a live boot Linux, shrink the primary partition and move it to the right
- Manually create the appropriate boot partition at the beginning of the disk
- Manually edit your BCD store to tell it to use the new boot manager
- Copy all boot files from the E:\ to the new boot manager
- Hope it works
Then when you move to GPT you will need a new EFI boot partition or convert the...