Ok so time is ticking on by so I am reducing the complexity by only using an Arduino Mega R3 with two 16 bit i2C expanders. This will achieve my short-term goals of 25 x 25 matrix with the flying probe. This will not be client/server, nor use configuration files. But it will get the job done and gives me my flying probe. All I have to do is wire it up the code is written for the most part. But I still have to write the flying probe code. Sorry for the mess in the wiring, blame it on Fritzing.