Hi Chad,
The developer guide is correct; JP1 is the 9-pin header that is closest to the center of the board. The early development samples of this board had these headers mislabeled on the PCB silkscreen, and you must have received one of these early boards. I apologize for the confusion.
Pin 1 of JP1 is the pin that is closest to the corner of the board. If you hold the board with the USB connector pointing up, pin 1 is in the bottom-right corner of JP1. If you use the keyed 9-pin programming cable and you follow our pinout recommendations on your custom PCB, everything should plug together the right way automatically.
To verify that you are connected to your custom board (and not the onboard xDot), you can remove the jumper from header JP30 and place it on header JP5. This un-powers and isolates the onboard xDot. Connect your custom board, and then unplug and re-plug the xDot DK from USB. If the USB drive shows up as “XDOT,” then it must be talking to your custom board. If it shows up as “MAINTENANCE,” then there’s still an issue somewhere. Note that your custom board will need to be powered up before plugging the xDot DK into USB.
Please let me know if there is anything else that I can help clarify.
Regards,
Tom