Alrighty. Your problem is that your hard drive has more than 1024 cylinders. This is not a linux thing, it is a MBR thing. Create a /boot partition on the beginning of the drive that is like 50 MB (yes, that is small, but all it holds is compiled kernel stuff). Then your / partition can be at the end of the drive if you want. Install LILO to the MBR, then you can edit LILO to point to the Win2k partition when you want to boot into it.
Please please please... Backup your stuff. And, if this is your production machine, you may want to consider doing this at some point when you have time to reinstall Win2k if you have major problems.

Questions? Post em. =)

j