Ford may claim a one time use on the J clips but I've always reused them with no issues, assuming they don't get destroyed when you loosen the bed up. Now for aligning the bed, depends how it is unaligned, side to side, up and down... Most likey it would be side to side, which is easy, loosen the 6bolts up about a 1/4 of the way and that will give u plenty of room to tweak it. From then on its a matter of checking down the side of the truck on both sides to make sure its even and adjust as nessicary. Once ur happy with the side to side check the gap between the front of the bed and the back of the cab, I usually just set it so theres enough room to stick my fingers in the gap. Next check the alignment of the rear to the bumper. Finally double check it all and tighten down the 6 bolts. Now if the bed if off as far as the height is concerned its a matter of adding shims to lift the bed up. A nice trick is to add some weight in the bed because I've found sometimes beds will twist and what looks good with the bolts loose changes quickly after you crank the bolts down. Once the level is set, adjust the side to side alignment and your good to go.