Get a front differential drop spacer from
Off Road Warehouse or I think
Wheeler's Off Road sells them too. this will get your axles better aligned from the diff to the hub.
Then about the rubbing of the Upper Control Arm with the coilspring, the only thing you can do is get rid of the 3" lift or get a set of Camburg or Total Chaos Upper Control Arms from either of the two stores listed above. These relocate the top of the steering knuckle out farther to allow a better alignment of the camber, caster and toe. They also provide an additional 1" of up and down travel.
2" - 2.5" is max for these trucks before you get to start spending some serious coin. once you go to 3" you need to get the others things too.