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CO was tested and set on the pot before Darren left, and nicely below 1% as I remember, and should be no reason to change that. I guess working on the basis of what could have been disturbed in terms of wiring when the turbo was swapped, then the tdc sensor cable is a possibility as it's on that side for the air intake, so worth checking that. Also check there are no poor connections / pushed back pins on the ecu connector. Check the chip is in and home, but if it wasn't you wouldn't be running at all, but always worth eliminating positively. Check reading of the air and water temp sensors back at the ecu connector, ecu disconnected, so checking for breaks or poor connections. As this is a sudden change in running, it's either water related or something disturbed moved in the run home. It was running clean when you took it away, and had been up the road for 10 / 15 min run prior to that, so the basics are there, something has changed in a step fashion.
You haven't got a dodgey flux capacitor have you, bit like JonV's?
So if you get it up on to boost, it runs cleanly does it?
Check the vacuum lines for leaks, pressure regulator line, MAP sensor line same.
Have you checked all 6 plugs?
The wires on Will's front lifter pump fell off in my hands when I was sorting his wiring, loose connection on the pump, and the road abuse of shock vibration the small gauge wires had fatigue failed (at the crimp tag); had this hit water, I think certainly one was likely to break as they dangle down and poorly supported by the factory fit arrangement.
Just some thoughts

Martin