Well - I finally got it sorted.
I drew out the whole system on paper and worked my way through it end to end. It possibly a culmination of things but the main culprit was the pipe at the end of the intercooler, it had come off just enough that I couldn't see it - but when I grabbed it to check it was firmly on I could pull it right away! I did remove and clean the MAFF as well so that may have helped.
Thanks for all the suggestions guys - I just didn't realise how much a small leak could affect how the car runs.
