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I'm just hard-pressed to believe you actually have a wiring issue in a 10yr old car. It's more likely the nodes on one end or the other. Since you've essentially proved out the end nodes, how about the points in-between...Have you ever replaced any of your relays? I replaced my 614 relays in the ECU...

I had knock sensor 1 replaced and flap sensors swapped between bank1 and bank2 to see it was a faulty sensor. After doing this the faults were still the same. When looking in VCDS, are you able to see knock voltage from the other sensors? Specifically what happens when you pull up knock sensor #1? ...

Couple things: -Is there a specific reason you're replacing the master cylinder? -"Uprated feed pipe from rob"? I haven't been on 246 in a long time, what exactly does this entail? The fluid feed hose from the reservoir to the master cylinder was typically replaced as a part of a TSB. Was this not a...

Bottom port connects to the purge valve. It looks like you've got that currently connected to the rear port on the IM, so swap that line. The rear-most port should be capped.

Doesn't sound like a wiring issue...looks more like one of the flap position sensors died (it should tell you bank 1 or 2 when you pull the code). The knock sensors are shared between cylinders (i.e. cyl 1 & 2 share 1 sensor). It may just be picking up noise from that area.