Just realised I never did update on this.
On my almost never ending journey, I discovered and talked to other people who had the same issue with these shocking designed pumps that seem to plague the vw (and Mercedes) range.
I went through it with another garage and a lead vw and Mercedes tech that worked there, and spent another £700 for the privilege of it (although, to be fair this did include a years ticket, and a new engine mount as they spotted the old one a bit worn).
I went through all the checks and things I had done.
The conclusion was that a voltage error seems to point to a short in the circuit, where the ECU sees a different voltage on the signal wire than expected. Apparently it is fairly common for these pumps to short out internally, as the electrics are not well seperated, and water can leak into the internal electrics and cause random short errors. This makes sense, as we went through my history of saved logs, and initially there was a momentary short to b+ and to ground on the pump before my problems started.
When the pump internally leaks water into the electrical part, the shorting can fire voltage back down the signal wire that is not expected. The ecu then throws such errors (note this can also occur if the wires are not installed properly following work such as clutch / flywheel. Note also, in my case first garage to replace the pump did notice wire to heater pump was strained, rubbing and not rerouted correctly by the original garage that did the clutch / flywheel).
In any case, we tried another new pump, at all locations, and my bypass loom at all locations. The same error persisted.
After further tests and data logging, all pumps are working as expected. This puzzled even the techs, they still thought it highly unlikely that an internal ecu error could occur or that the ecu was at fault. They had only seen one ECU failure in all the issues they have had with these pump circuits.
The end result was, another pump as front EGR cooler sounded ‘weak’, and tested all signal wires / scoped, proved to be OK. So they updated software and coded out the specific error from the ECU. ECU will still report other shorts should the circuit fail (short to ground, b+ etc), just not supply voltage problem that seems to be stuck. The van works perfectly fine and has done even with this error since last November!
The other option on the table was a new ECU as well, but even though everything was working (also no water ingress or damage to ecu on inspection). They still believed replacing ecu was not worth it.
Bottom line, the pumps are working, circuits are fine, ECU otherwise seems fine and the error is gone.
Good luck to anyone else troubleshooting the same error in the future. I spent over £1000 on this and countless weekends and evenings!