If the hardware in the two systems is identical (with the exception of the hard drives), then swapping the hard drives between the two systems will give some additional insight.
If the slow shutdown moves with the hard drive, then the cause is the hard drive or something in the w2k install/setup on the hard drive. If the slow shutdown does not move, then it is a hardware or bios (motherboard, video board, network card, etc.) related.
If you had a third hard drive to experiment with, you could clone (or ghost) the contents of one hard drive to the third and install the third and see what happens. Then cloning the other hard drive to this third one and again seeing what happens will give additonal insights. Of course, you could forget about a third drive and just clone the fast shutdown drive to the slow one and see what happens, assuming that you do not mind losing the software/setup that is unique to the cloned-to drive prior to cloning.
If they are both networked together, try disconnecting BOTH from the nework (remove the network cable from each network card and restart both systems. When they are back up, then shut down each one and time them. It may be that the difference in shutdown time could be due to networking issues at shutdown.
Paul