You should be ok with the 2" spring lift and the 1" body lift. How big of tires are you going? if you are going 33 or smaller I would hold off on the body lift for now. Untill you see if yoou need it. I haad 33x 13.5 swamper's on my tj for a while, they didn't rub but I had other issues,
There is always a chance of getting some driveshaft vibration at 3" of lift, some people do, most don't. Usually vibrations come with 4" or more lift then you have to look at getting a slip yoke eliminator and new rear driveshaft.