OK, so i got my alternator, surging issue taken care of. My stock ECU has something very very wrong with it. It was messing up the voltage going to the alternator, and causing the surging problem. So i got underneath the car, took out the harness that connects the alternator to the ecu, clipped the wires, and soldered them together. This successfully made my alternator a stand alone unit.
Next thing to be disconnected from my ecu, the coolant temp sensor. We are getting crazy readings on the AEM from the stock sensor, so we're going to cut it out of the equation once again, and see if it fixes my fan problem.