One thing it could be is the GEM module. I seriously doubt that a surge would take out all that stuff without blowing a fuse. Has your dad jump started anybody lately? The GEM module, along with the PCM are sensitive to damage from voltage spikes. Before replacing the GEM module, I would try resetting it. You can do this my disconnecting your negative battery cable,
and touching it to the positive battery cable (negative battery cable is off the negative battery terminal). This will remove power from the GEM module,
and discharge the internal filter capacitors......