Is windows telling you it can install because your drive contains an MBR when it should contain a GPT? Here's how you can get around that:
Use an Ubuntu Live CD. I personally use an EFI thumb drive.
Stick the drive in, reboot, then press & hold `option` once you here the Apple boot chime. You'll get a few options and you can select EFI then boot into live mode.
Once in the Ubuntu OS open up a terminal and do the following commands:
For the first step you need to pick the drive with the issue. Mine was /dev/sda but your's may be /dev/disk0. You're safe to guess because we'll double check the drive info to make sure it's the one you want.
$ sudo gdisk /dev/sda
press `?` to see the help menu
press `p` to see your current drive's details. If this is the wrong drive then press `q` and try again.
press `x` to enter the experts menu
press `n` to create and new protectve MBR
press `w` to write these changes to disk.
Remove the Ubuntu Live media and insert your Windows EFI boot media Reboot and hold option at the chime again. This time select your Windows EFI boot and the setup should be pretty standard from here.