After all of your diagnostics, repairs, and troubleshooting, one fact still remains: The symptoms are still present due to the systems inability to maintain voltage properly. You have two choices: #1 Take the vehicle to a shop that has equipment capable of testing the alternator/regulator output on an oscilloscope. Short of disassembling the alternator and checking each individual diode, the only way to accurately diagnose a bad diode is to watch the sine wave pattern on a scope. Then replace the alternator. Or #2 you can just replace the alternator with a good one and save yourself some time and money. This is not a "Phantom problem" that you're experiencing, you have a bad alternator.