I haven't installed windows for a while, but why don't you just install it on the second drive, with the first drive un-plugged? Then, as long as the second drive is partitioned similarly, you should just be able to plug in the first drive, and the world will be a happy place, again.
note: you might need to edit grub's menu.1st file, but as long as the partitions are aranges the same way, everything should work. I don't believe the partitions would need to be the same size.