Problem: A circuit or subcircuit where you need to flip off two breakers to turn of one particular light or one particular half of a duplex receptacle; either one of the breakers turned on keeps it alive.
Short term solution: You should immediately unhook the circuit wire from one of the two breakers in question, label it, and tape it over, and then you can find out where the wires are crossed at your leisure.
After unhooking the wire, you may notice that certain built in and/or plugged in lights controlled by those breakers flicker. Stop using them as you find them (except for a few seconds of testing if you find another) and label the respective light or receptacle half. You may find enough of them to more or less trace the circuit to the place where a loose cross connection is.
The average homeowner who lost his house in the Oklahoma tornadoes should move for good and not rebuild. Too much complexity watchdogging the contractor. Too much a chance to be defrauded.