Chipstein, I am not familiar with the covers that clip on. Several of the guys in the local group have the 01's so maybe some investigation in in order. Sounds like a bandaid fix for rough surfaces and/or out of tolerance knuckles or calipers. There is a specific gap between the two that must be maintained, with a min and max tolerance. I believe that it is . 080-. 125" total gap, but check a service manual to be sure. Too little or too much and it will bind. If I could omit the clips and maintain the tolerance I would try it, but be sure it is in spec if you take them out. If the clips are smooth and not causing a bind I would leave well enough alone and leave them in.
Sqealing is a tough one. First I would try whay Bob suggests with also sanding the rotors and pads a little, just enough to take the glaze off is fine. 100 grit paper on a DA sander works great for this, just keep the sander in motion.