Where was the noise coming from? Chain rub on the front DR is more on my new bike with Ultegra Di2 than it was on my Paramount with Shimano 105 5800 11 speed. The chain stays are shorter on the Tarmac so the chain is more angled so it isn't easy to get it quiet from chain rub.
Changing wheels probably just put the cassette in a slightly different position and maybe more to the bad side. But if you run your Di2 in full syncro, then it'll never be in the Big Big combo that gives the most fits. And you'll have a better chance of getting the noise adjusted out if you are having rub in the small front/ big rear combo.
As for the brake, the body of the brake has slotted holes. So just loosen the bolts holding it to the frame and you can adjust it if needed. If you are going to be swapping wheels, then you might need to shim the rotor or hub to one side. Or start bending the rotor and have fun! However if it's just the pads and not the brake body that is in the way then push the pucks back in the cylinders and they'll figure out where they need to be after you actuate the brake lever a few times. After the wheel and rotor are in place of course.
Last edited by Iride01; 05-06-22 at 02:27 PM.