Installing Windows will overwrite the MBR anyway (had this problem some time ago). The way you can get it working, is to physically UNPLUG the drive with your Ubuntu, by completely removing it from your computer, then installing Windows on the other drive, and re-plugging the drive with Ubuntu.
This way you will be completely sure MBR will be okay, for Windows installer will have absolutely no access to the drive with Ubuntu, as it will be separated from your computer (but some people advice it is even safer too temporarily keep the unmounted drive in a separate room, just in case [not really, I'm just kidding]).
This way you will get both systems installed on separate drives. After re-plugging make sure to alter your BIOS setting - you want to start the boot from the Ubuntu drive, as that's where GRUB is. Note that on first boot you will (most probably) not have an option to boot Windows. To fix that, boot into your Ubuntu and run
sudo update-grub, this should detect Windows and add it's entry to the boot menu.