That may work. If not you may have to boot from a Linux floppy and make a change or two.
I would do this. Remove the drive, windoze drive, and put in the drive you want Linux on as the Primary Master. Install Slackware and such then put the drive in the other system and return the windoze drive back to its proper place.
Done that way lilo, or grub, and the fstab files should be correct and your MBR will not be messed with on the windoze drive either. Don't forget to change your BIOS when you change the drives. It may get
and do a bit of
and you may
Did that make sense? I just don't know how it will work if you compile the kernel and the machines are really different.
You will be the one getting wet here.