blairallday:
I think it's going to be tough figuring out whats going on in the PCB in respect to both the hardware and software.
That software part is new. From your opening post, you wanted to intercept the signal; and that can easily be done once you have an understanding of the board. The board has 5 similar groups of connectors (POD1 .. POD5); once you have figured out one, the others will with high probability be similar.
Next determine the type of the 16 pin chip; I suspect that it's a multiplexer.
Is you yellow connector the only one connected to the board? Or do white, blue and red also have connections to your external device(s)?