Where can I find the OPUploadTool?
Good question. I recall there is a build problem with it, but maybe not back in 16.09
Even if the baud rate was wrong I should still see some data on the Tx line with the scope, but there's nothing there (GPS only mode does show data on the scope).
Well, I think that leaves out the baud rate as an issue, the mag data should be there at least. Last hope would be reflashing the MCU.
I would try to diagnose a hardware issue, but I can't really do that without a schematic or net-list. Is there a chance that information is floating around?
A schematic was apparently never released. There are one or two people who make them (for like $100).
First trace the TxD line back to the MCU and see if you see data there, but not on the connector pin. That might be a simple fix. I think that SBL running puts data on TxD without being prompted from RxD, but it's just a guess. You could put a solder blob across SBL (system boot loader) and see if you then see output (using the scope) on the MCU pin with the SBL active. If so, you can try flashing firmware. If not, best hope might be replacing the MCU then flashing.