Let me be clear, pin 21 from the ECU is irrelevant. According to the wiring diagrams I have (both OEM Audi and Mitchell1) pins 21-24 are not used. Let’s not waste further effort chasing pin 21. (I have attached the Mitchell1 diagram at the bottom of my post).
So now that you have determined you have power and ground to the ECU, that pretty much limits you to two remaining possibilities: 1) The ECU is faulty (not likely since you swapped to another ECU with the same results—but not impossible) or 2) something is corrupting the CAN BUS signal from the ECU.
Normally the way I would diagnose a CAN-BUS issue is with a breakout box and lab scope. However, with limited tools there are still ways to narrow down the problem. Without going into too much detail, the CAN lines transmit a square wave signal between 0-5 volts (CAN high is from 2.5-5v and CAN low is from 0-2.5v). What I have seen on no-comms (scan tool cannot communicate with the ECU nor can other modules) in the past (but not specifically Audi), is a malfunctioning module can send a steady 5v onto the CAN lines corrupting the signals to and from the ECU. Or alternatively it can ground the CAN line. The way to test for this is by unplugging various modules until you can communicate with the ECU again.
I would start by hooking up my scan tool (or perhaps just turning key and looking for check engine light) and confirm that there is no communication with the ECU. Then I would disconnect the ABS module, cycle the key and see if the check engine light illuminates and you can communicate with the ECU. Next I would unplug the MAF, then throttle body, EGT sensors etc... until you either run out of sensors or comms return. Remember to cycle the key after unplugging each item. Basically, any sensor that has a 5v reference feed is what you want to unplug. These are almost always three wire (or more)sensors. You can use the attached wiring diagram to give you some ideas of what to unplug. If there is a faulty sensor bringing down the CAN signals, unplugging it should restore communication from the ECU to your scan tool. Obviously the last item unplugged before comms are restored is where your issue lies.
Also note that a short in the wiring harness somewhere could also be the source of a corrupted signal. But usually you should be able to identify chafing or exposed wires from the engine wiring loom. Here is where having an oscilloscope is a big advantage. You would be able to visually see the signals (CAN high and CAN low) to see if they are being pulled to ground, driven high, or corrupted (no longer a square wave).
Keep at it, you will solve it eventually.
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