As an electrician, I can say without a doubt you have gremlins, and they're absolutely a poison to your happiness.
General troubleshooting methods and procedures can be helpful here. Start at a point that can be traced. For instance, take both your batteries and have them checked. Afterwards run continuity (ohm) checks through your positive and negative wires and record their resistance readings.
Then take alternator, have it checked. Check voltage regulator at this time.
You have too many small issues for each thing to be it's own problem. ECU's require seeing a specific voltage to operate correctly and I think your charge system is the fault here.
It's also not healthy to keep all of the egr equipment if you don't have to. Depending on your mileage that can be hindering engine performance, which will only exacerbate voltage drop issues when components don't recieve what they need.