To get the DigitalMod to do something on startup, you have to create a scripted overlay, not a scripted module. Overlays are global and thier events will fire regardless of where in streetdeck you are. Just overload the OnCreate event and put your COM code in there.
The options are stored in options.sdo. XML files use to be used, but were too slow. This is a binary format file. The GPS com port should be the 47th integer in this file. The integer size is 4 bytes. The file format very rarly changes, but I can't garuntee if you read the file in yourself that it will be compatible with all future versions.