Check the LG/W ( light green with a white stripe) wire from the ECU's big terminal to the alternator.
It's right on the end of the big terminal.
Being as you've already found some bad wiring, it would be smart to check that wire before replacing your alternator.
You could try checking the voltage at that terminal with the car running to get a reading... It should probably be between a few volts and 12 volts.
Probe between the backside of the terminal and ground. Then see if the voltage is making its way to the alternator and check for voltage where it plugs into the alternator.
Doing it this way is difficult because the car needs to be running and that can be dangerous.
The better way to check it is to clip a ten foot piece of wire to one of your leads on your Ohmmeter and check for resistance/continuity.
With the car turned off, unplug the LG/W connector from the alternator and clip the long lead to the connectors terminal... Then go inside your car and unplug the big connector from your ECU and test for resistance across the LG/W wire.
The resistance should be 0 or close to it.
You need to unplug both of the connectors to get your reading or you may get a reading of the circuit it plugs into.... You need to isolate the wire.