I don't know where else to turn but there are some very smart people here who can hopefully give me some hints.

Engine is a 2002 ALH TDI with a 038 906 012 FF (or FD, I have two ECUs to work with). IMMO3 disabled via full version VAGdashCAN on both ECUs. Vehicle is 1986 VW syncro westfalia

VCDS (v11.11.4) USB-HEX-CAN communicates just fine key on, engine off. I scoped the k-line with our picoscope/breakout box and it has a normal waveform.

When I try to communicate with the engine running, VCDS comes up with too many communication errors. It usually manages to pull the ECU part number off and once pulled the full information and lit up the buttons. When I scoped that, the k-line voltage rises up to alternator voltage ~14v but instead of the waveform dropping slightly to almost ground while communicating, it falls on it's face, full ground signal for a significant amount of time. Only once while VCDS is trying to open the ECU does it give me a normal waveform (very short amount of time). So it's obvious I have an issue with the k-line.

CAN high/low lines communicate pretty much the same with engine running or not, but they only go to the ECU and DLC, no where else since it's an engine swap.

I have tried adding in another ground to ECU connections, unplugging the wire to the front DLC, different ECUs, multiple tools (VCDS, superVAG, Launch, I'll try our 5052 once the battery charges) and everything says the same thing.

Anyone have any insight into this? I scan cars all day long at work with my VCDS cable, never any issues so my hardware on my PC is correct.

I tried some things with one ECU tonight and ended up frying something inside that communicates. It still runs the car but won't talk even key on, engine off.

After two months straight working on the swap after work and on weekends (that means 12 hour days, almost every day...), I'm ready to abandon it for a while and get it out of my sight for a few months. It's tough because my day job is figuring out issues like this on the same cars, but they have all the modules intact and IMMO not deleted.