After talking to the creator of the board, I hear that the corner pads do not matter.

I had damaged the corner pads, so I tried to extend them with a single strand desoldering braid wire.

This lifted up the board however. This could have made the through hole via to the bottom of the GPS module pad connections difficult.
I filed down a razor blade and was able to fit it between the GPS module and the PCB board. I suspect that with the razor blade and a desoldering iron I may be able to push the desoldering braid out of the way.


This could make the board functional. As it is, if I power it up I get a single flash on the HM-TRP module of both the green and red leds, but no following flashes. I think this is due to a short or possibly a non-existent connection to one of the bottom pads of the GPS module.
http://www.hoperf.de/upload/rf_app/HM-TRP.pdf (page 7). The GPS module may not be able to send data to the HM-TRP module.