->  RJT> There's a PS/2 pin header up by the keyboard connector I'm
prepared for

-> You sure?  there are at least three arrangements I've seen.  A
-> single line, and two versions of 2x4 or 2x5.  Don't be surprized
-> if it doesn't work, but that might just mean you need to rearrange
-> the connector.

Same with USB MB connectors. Some have pin Pin one on one end of the
Double row of pins and some have pin one on Opposite cends of those two
rows.

->  RJT> In between the first and second PCI connectors is another
->  RJT> pin header,  2 rows by 9 pins long,  missing one pin.  I
->  RJT> have *no* idea what this one is for,  anybody know?

-> IR, I'd bet.

I supsepct that is the Case Front panel connector. 
IR only takes 4 wires
--- Platinum Xpress/Win/WINServer v3.0pr5