I don't think I understood correctly, you made the connector? If you bought a gps for the PXFMini from us the connector should be a-ok and the gps tested. We solder the different cables to modify the default connector (by default the output is 2 DF13 connectors) for the PXFMini's JST connector.
To verify the board is getting data from the GPS (to test the connection between both, not that the GPS gets a fix) you can run the following command while on the device (either connected through SSH or directly with a keyboard and display):
sudo screen /dev/ttyAMA0 115200
You should get scrambled characters on your terminal (either squares or gibberish), that would indicate the connection works.
Please clarify what I quoted and tell me if you get the expected result when executing that command.