Your new rims wouldn't cause these problems unless installed incorrectly, for instance, not all the way tightened or balanced correctly.
Do you experience vibrating in your steering wheel ALL the time? Or is it only when braking?
Sorry, I dont own a 5th gen, but I would like to help.
Well, don't wait until 1 mm of thickness to go change them. At 1 mm you are transferring a lot of heat to the rotor. I would change them once they get around 2.5 mm.
I am going to shoot out some rough estimates, but the factory pads offer more padding than aftermarket at time, so their roughly between 10mm and 12mm.