Yeah, that should work fine. If you put yourt boot partition and boot loader (use grub) on the pen drive, I think it would be easiest.
grub> root (hdx,0)
Where the x in "hdx" is the number that represents your drive. You may have to play around until you find the right number.
Hope this helps a little, and good luck! (google around for grub if you need help with it).