Colin.
You mentioned long motorway journeys so I assume the pads have bedded in by now.
Is it definitely the discs that are the source of the heat, rather than the wheel bearings? If so, the pads must be rubbing, which points directly at the changes you have made to the braking system. Are the new parts standard Audi components? Thicker than normal pads and discs are a possible explanation, but I fancy it is more likely the pistons are not retracting as they should.