The example program I can offer that might help you out is the mavlink-socket example found here. Take a look at that and see if it helps. It's a program that runs on the COM that communicates with the AeroCore.
I don't have any specific examples about WiFi/Bluetooth. It depends on what version of kernel you're using. Assuming you're using a recent version, you can find lots of examples/tutorials online. If you have trouble, try to ask specific questions.
The GPS (PreGo board) is plug and play with the AeroCore. The stock AeroCore firmware will communicate with the GPS and using the onboard IMU it calculates the position. Again, please be more specific in your questions if you're having trouble.