Just for some closure to the thread, and in case anyone else has a similar problem. It took me some time to come up with concrete proof that there was an actual problem which basically involved getting my own OBD reader and scanning the test result logs. Turns out that the ECU was recording misfires on cylinder number 1, at which point I booked it in with Audi to be fixed.
The problem ended up being that somehow a bolt (which looks a lot like the ones holding the plastic casing around the cam shaft pulleys to the head) had found its way into the cylinder head and damaged the number 1's lobe on the exhaust camshaft. The only way in, if not present from manufacture, is through the oil filler cap. Unfortunately, because I'd had the clutch changed and bigger intercooler fitted not long before it went into Audi they pointed the finger at the "3rd party garage" and took no responsibility. In a nut shell, irrespective of me moaning about and having evidence of trying to diagnose a running issue several weeks before that work was completed they still told me to get lost. The bill for replacing the exhaust cam, oh, and a new injector they tried came to 3 grand. To give them their due they had spent 33.8 hours on the car from start to finish but only billed me for 17 hours at a reduced rate. In affect their way of going "50/50" on the issue.
I got my car back from Audi yesterday having been there for the best part of 2 months. Seemed a bit sluggish at first but it felt better after some time ... and then this morning, engine management light: po420 some garbage about the cat but could be many things causing emissions problems. So next week its going back in to have that sorted out. ***.
An expensive lesson in why not to muck about with your car in any way at all if you want to use the approved warranty, including using a cheaper garage to fix a failed component not covered by the warranty (clutch), because if they can get out of paying up for an expensive repair then they will.
I'm still looking into whether its worth taking them to court under consumer law: the car not being fit for purpose at point of sale. As it was reported within 6 months of purchase the onus is on Audi to prove it didnt exist when I bought the car, and Im not sure they can. Their diagnostic check pre-sale shows no misfires, but that doesnt prove the bolt wasnt already present inside the engine or hadnt already done some damage to the shaft, which would worsen over time with use. Unfortunately for me, the earliest recorded misfire in the ecu's "unwipeable logs" (according to Audi) was some 10 days after the clutch change work which conveniently makes it look like it was caused by the garage (even though they didnt go near the filler cap). However, I know 100% that some issue existed well before then and the same symptoms have persisted throughout the ordeal. perhaps the damage just wasnt bad enough to register a misfire until later but this really has not helped me at all. Despite the onus being on Audi, I think if it went to court I would have to somehow show that the lack of recorded misfire at point of sale isnt enough to prove 100% that the physical problem didnt already exist to some extent. I will be seeking legal advice on this.