What pads did you get with your Alcons?
I'm betting Ferodo DS Performance/2500s?
I'm then betting you've got them hot, they've melted and they've smeared themselves all over the discs, causing loads of high spots and they're now juddering like hell?
Mine did the same thing.
They're utter, utter sh*te pads. They can't sell you a road kit with a non-Emarked pad... thing is, Emarked pads suck ass. You will not have warped the discs, I guarantee it - I've had zero problems since changing mine and had them glowing, they're not so much as glazed.
Going back to the original problem, I had the discs re-polished (not skimmed) and junked the pads in favour of Carbotech XP8s. I also use Carbonne Lorraine RC6s on my other rotors, basically you just need to choose your compound wisely as you've got hugely powerful brakes capable of generating a lot of heat. Speaking to Alcon may well see them sort the discs and pads for you as a means of goodwill.
The Audi set up? Waste of money IMO. They're for a 600kg+ heavier car, won't be running the right sort of piston sizes to suit your M/C (i.e you'll get a crap, long pedal and on/off brakes) and you'll never get enough heat into such a big disc to get them working well... heat in brakes is good.
You've a good set up, I'd think about what I've said and talk to Alcon before jumping out of them, as you'll regret it.
EDIT: I'd say the same thing if they were APs, VWR's, Brembos....... it's all down to the crap pad.