I'm going to ring Audi up tommorrow and get them to look at it, still under warranty til next month and they seem to be good when it comes to warranty claims (had steering rack, air con comp and both seat bases done in last 7 months with all mods on) The stuff i've had replaced all have been things that my mods shouldn't effect anyway so they might spit their dummies out with this one due to the engine mods my car has. I work in the car trade myself so i'd say that they might do it if its a common fault.
The more I drive it the more I think it is the coil or coils, I sell loads where I work and it seems to be a problem on all new engines, coils on petrols and EGR valves on diesels.