Basically, it's more trouble than it's worth having two different systems trying to handle the same thing - I'm talking about the serial communication between Arduino and Chipkit. It does work, but it's only a matter of time until it becomes unbearable sending information back and forth, not to mention the very limited RAM in the Arduino.
I'll most probably only use the Chipkit since it's got plenty of I/O, lots of RAM and overall a beefier MCU. After the converging of the boards I'll have to see how many inputs/outputs there are left, but most definitely I'll have a couple to spare. There will be some pretty nasty refactoring of the code thou...
I've also decided that I need to build a switchboard and a light board -
The switchboard will give me 64 switches instead of the old one with 32 inputs.
The new one will also feature cable connectors so that there's only two flat-cables to unplug instead of 32 independent ones. Much simpler and much less to keep track of. They will still be 64 independent switches and not a matrix, so each switch gets it's own connection. In theory I could matrix these switches to create 4096 (64*64) switches...
The lightboard gives me 96 independent digital outputs for lights.
The old MUX-shield I planned to use only gave me 48 outputs and for some reason I cannot explain - it does no longer work. I'm actually not sure if I've ever tested it in with the Chipkit (+3.3VDC vs +5VDC). Since it's an output board, each of these outputs could in turn trigger a MOSFET to turn on/off a series of lights, instead of just a single light. This board will also use two 50-port flat-cables for quick and easy disconnections. The two extra ports in each cable will be additional ground lines.
The main power output of the lightboard will be controlled via a relay, so no power is sent to the outputs unless it's told to by the MCU. Purely for safety, and not sure if needed - but I had a relay to spare. The increased number of outputs allows for much more lights, and that's a good thing!
The best thing about these boards I'll be making (parts are ordered) is that I'll only trade 3 control pins for "any" number of inputs/outputs required. This means I could hook up another identical board to gain an additional 64/96 inputs/outputs. Sweet!