Multiple LED's on separate pins, switches and functions - need guidance

PaulRB:

HolidayV:
despite what the data sheet on the $3 pro mini's says, it cannot handle 12v

How much current were you drawing from the Arduino? It should have been OK as long as you don't draw more than a couple of hundred mA.

The whole circuit is drawing about 500mah. I hooked it up to a 12v, 9800mah li-ion battery with about 50% charge on it outputting 11.4 volts and the lights came on for 2 seconds and then the ATmega chip put out a pretty little puff of blue smoke.
I rebuilt the circuit last night putting an LM7805 between the battery and vcc of the arduino and it works great now.