My parts finally arrived. I ordered a GPS logger from Adafruit and a uBlox5 GPS from DIY drones. Ublox has a program uCenter used to configure the uBlox5 GPS. The uCenter user guide is here. The GPS comes with an adapter so that it is compatible with the EM-406 type cable. So it works with the data logger which was designed for the EM-406.
Tonight I soldered the components on the data logger board and fired it up with a FTDI cable. The uBlox5 ran at 9600bps. You can get it setup in several different ways from DIY drones and I chose standard NMEA, because the code from Adafruit parses NMEA sentences.
The Arduino serial monitor started spitting our NMEA without a hitch. I was kind of surprised that it just worked.
I chose the uBlox because its very highly regarded by the people over at diydrones and it has a refresh of 4hz, and resolution with WAAS of 2 meters.