Yea....there's PLENTY of wiggle room on these trucks. Just loosen up those 6 bolts, move the bed around to get it aligned perfect to the cab. Then you should be good to go(obviously after bolt tightening of course). Not only is there wiggle room in the 'nut' on the frame, but there's also wiggle room with the bolt to hole size on the bed itself. Just get out there and get to work. You won't hurt anything. I assume the bodyshop pulled the bed off to replace the bedside, and lacked on getting the bed repostioned perfectly.
'01 XLT disguised as a '03 Fx4 Level II
Big. Loud. Slow. Bright.