Wow, long thread. I just skimmed through it, so I probably missed half of it.
A couple of notes. gpsapp sets the baudrate on the serial port when it opens it during startup (nmea & earthmate use 4800, trimble tsip uses 9600 etc.)

I've had trouble myself with having the [gpsapp] section in config.ini. Just try to pass the protocol on the command line, i.e. start it as 'gpsapp earthmate'.

Finally, the serial connector on my sled turned out to be not entirely swapped, things worked with a null-modem adapter when the cable only passed RX,TX and ground, but didn't work right with a full cable. In fact it looks like only RX and TX are swapped, but the rest (RTS/CTS/DTR/DCD) are in a straight through configuration. So the best thing to try would be a straight through cable with only RX and TX swapped.

You can derive power from one of the serial pins, I forgot which but it is in the faq somewhere. But you can't just plug a 12v->6v transformer in the middle because it is a DC current, and the transformer needs alternating current to work. I used a PT-5101A, which is a switching regulator that turns 9-38V into a stabilized 5V without turning half of the drained energy into heat. However this part is pretty expensive and the 6V one even more so ($15), so you'd probably want to go for a simple 7806 regulator.

Also your picture was strange, why was (+) connected to the GND, and the (-) to the DTR pin on the gps?