I'd be taking your car to somewhere like Harding Performance or another VAG independent specialist for diagnosis. Armed with that, then go to the dealership for them to asses it, see what they say and what warranty work they will carry out.

To me, it sounds like your mechatronics unit is on its way out RE rattle and clunk, the shuddering at idle could be either fouled spark plugs or a coilpack on its way out... Both known issues. I'd pull each spark plug out and asses them, even take a picture of each one and post them up on here.