RIch,
You know what I have gone through with my S3 hesitation problem. At the moment, nearly 2 weeks after Torquing up the plugs, I have not had the hesitation. The car is bang on performance wise, it is truely unbelievable. Its like a rocket at the moment.
My list would be:-
1) Check your DV for smooth operation.
2) Check your hoses, VAG-COM requested & actual boost, although if your mega modded like you are, IIRC it won't read correctly. (is that right?)
3) VAG-COM misfires, logging all cylinders not just sum of misfires.
4) take out the coil packs, check for discolouration and fitment. Do they fit snug still?
5) whilst coils are out, look at plugs, colour etc. Do they look healthy. Change 'em if they've not been done for a while. S3 ones should last 40K, but if driven hard, or mega modded like your self, it might shorten their life.
6) re-fit plugs Torque them to 30Nm .
7) re-fit coils etc etc.
8) Is the car any better? f not then check the MAF. Unplug it, is it any smoother? does hesitation occur.
9) Perhaps clean the TB, and do an TB adaptation. I do this as a last resort, as when this is done, my car runs fine for about 3 weeks, and then hesitation comes back. (PS. when i did my plugs, i did not do an adaptation, didn't want it to skew my testing.)
After that, you know the usual stuff, N75, N249, inputs to EPC, brake pedal light switch, clutch pedal switch, accel position sensor.
good luck
AL