I went through the resource assignments of the hardware on both systems to compare. Of notable interest, Win2k does not assign an IRQ to the unused secondary IDE controller, whereas Win9x does. I will post a list of the data below if it of any use.
Resource Assignments
Win98:
Primary IDE
Input/Output Range 01F0 - 01F7
Input/Output Range 03F6 - 03F6
Interrupt Request 14
Input/Output Range EF00 - EF07
Secondary IDE
Input/Output Range 0170 - 0177
Input/Output Range 0376 - 0376
Interrupt Request 15
Input/Output Range EF0B - EF0F
Dual PCI IDE
Input/Output Range 01F0 - 01F7
Input/Output Range 03F6 - 03F6
Interrupt Request 14
Input/Output Range 0170 - 0177
Input/Output Range 0376 - 0376
Interrupt Request 15
Input/Output Range EF00 - EF0F
Win2k:
Primary IDE
Input/Output Range 01F0 - 01F7
Input/Output Range 03F6 - 03F6
Interrupt Request 14
Secondary IDE
Input/Output Range 0170 - 0177
Input/Output Range 0376 - 0376
Dual PCI IDE
Input/Output Range EF00 - EF0F