I'm guessing here, since you haven't provided a circuit or code, but you say that the problem started after the 12V power "fried". That could have caused many types of partial failure in anything that was connected at the time - some parts of chips could have received reverse polarity for a short while, PCB traces that burned out could have temporarily or permanently shorted to adjacent traces, etc.
The less tedious way to go from here would probably be to start from scratch with entirely new components and PCBs. The possibly less expensive, but far more tedious and frustrating way, would be to perform step by step fault finding through the entire system, but without a circuit diagram or the Arduino code, we can't really give any more specific advice on how to go about doing that.