I don't understand why the battery seems so distant in your electrical system. It obviously has enough power to supply the starter. And to run the computer and the ignition system.
But when it comes to absorbing anything the alternator may dish out, the battery is not taking care of it. If the alternator went wild and went full output charging, the battery normally absorbs this. The battery may get to 16v or a little higher, but it takes care of it as long as it can before it starts boiling and has a meltdown. The electronics of the truck can handle 16-18v.
If the alternator had a A/C component in it's output because of a bad diode, again the battery acts like a large tank, absorbing any spikes in the voltage.
Most of the time very weird things in a vehicle can be caused by a bad ground. I have seen melted ecm ground wires because the main large ground was bad. The alternator uses the engine block, and the engine block uses the large ground to connect to the battery. If this goes bad, it will search any wire it can to try to ground itself back to the battery. But usually when this happens you will have melted, smoking smaller ground wires. But you have been all over this thing lately, I would think you would have come across any smoking melted wiring.
This is a tough one.