Is the issue here that Ubuntu is already installed and Windows is not? If so, it should not be difficult to ditch your current Ubuntu setup and re-install, as long as you back up all the volatile directories somewhere for later retrieval... these are things like /var, /home etc.
At which point the simplest way is... a. install Windows on master drive b. install Linux on slave drive, let it redo MBR for Windows drive (ie. dual boot) c. restore volatile Ubuntu data (eg. /home directories and installed applications) Sean
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