UPDATE:
Dealer called back and is ready to fix all the small stuff...good deal.
I took a tape measure to the truck, and to my surprise, the bedside that was replaced is the same distance from the frame on both sides...heck, it might even stick out 1/8" more on the p-side. So, I measured the wheels. My axle is shifted to the right, that is why it looks so odd. I'm guessing they had to drop the axle to put the exhaust on, and got it messed up when they put it back together. I have to say that should be easily fixed, and made me have a sigh of relief.