Code that "breaks" arduino

sbrown:
I have the design all figured out,

That may be, but you haven't ever fully described it and shared it with us.
My suspicion is that if you really had it "all figured out" you wouldn't be asking all these questions and wouldn't have blown up your Arduino boards.

I just don't understand these new coding terms. Besides, I can make a different copy of the code. So instead of using 5V you're saying to use the other pins on the arduino?

Not exactly.
You manipulate a pin on one end of the wire and watch for the change on a another pin on the other end of the wire.
That said, No pin is ever driving a 5v output signal like your direct connection to 5V.

In non coding terms, you want to create an open drain signal or "bus" on your wires.
You use the internal pullups on the AVR pins to create the high level signal on the wires and use a pin to drive the signal low.
You NEVER drive the signal high with a pin.

When done this way, the low output from the output pin on one end of the wire has to travel through the wire to ground the input pin on the other end of the wire in order for the input pin to see a low.
If the wire is broken, or the output pin is set to input mode, the input pin reads a high from its internal pullup.
And you never have to worry about a high level output shorting to a low level output since no pin ever creates a high level output.

In terms of Arduino:
setting an Arduino pin mode to INPUT_PULLUP sets the pin to input mode and turns on the internal pullup.
setting an Arduino pin to OUTPUT will set the pin to output mode - and if you have not ever written to the pin it will default to LOW.

--- bill