This is going to be for the ground station, which will be handling a majority of the data collection along with running the web server for data display.

I am thinking that the device should be based around a smaller linux based computer system, I wonder if that exist...

The Raspberry Pi has a huge amount of capability, especially when it comes to communicating with some kind of slave interface. This can typically be done with a couple different I/O options, but the one I am thinking about is the GPIO bus.