Hi black jack, thanks for the comments. The air filter is fine. My turbo must be fixed vane as it has a waste-gate. Don't forget that all these faults disappear when the ignition is turned off then back on.
Surely if the inlet manifold is so badly clogged the fault would be there all the time.

I can replicate the fault by disconnecting the air temp sensor on the inter cooler. I am going to check the wiring for any breaks. Also next time it faults I'm gonna lift the bonnet and check for +5v on these 2 wires which it should read when working. If no volts then possibly a fault in the wiring.