Different UEXT signals on EMX and FEZ Cobra

I’ve been told to add a WiFi connection to our design for future use, using the UEXT connector so it will be compatible with the GHI WiFi module. I have the connector and pin-outs from the FEZ Cobra Eagle files, but we also have the EMX Dev system for development work, and the UEXT connector on it has different signals.

Which should I use for the new board for best compatibility with the WiFi requirements?

Either one will work just fine. For long term, you should use the new gadgeteer type connector. It is 10 pin but with 1.27mm spacing and different pinout.