Windows 2000 takes fewer resources to run. If you had just cleaned the unneeded software off, and kept the older operating system, you might have noticed a faster response time.

Win2000 is more than adequate to run a file server.

You can find out if you can 'overclock' the chip. The faster the clockspeed, the faster the computer.

You can find out if the motherboard will take a faster chip.

But I wouldn't screw with the hardware too much. Hell... if you could get away with it... try going back to Win98. (I just don't know if '98 supports this kind of server.)