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When I got home I also noticed that there was new bolts fastening the truck bed down and could tell that the old ones were grinded out. This triggered me to look more closely under the truck and I noticed they replaced the shocks and spray painted most things black. After seeing this and already knowing about the door issue it becomes very clear that this truck was in an accident of some kind that wasn't reported and the frame of the truck is likely tweaked.
I followed up with the dealer today to see if they would make things right but they said they would not do a return. They said the bed was taken off to replace the fuel pump which means they lied to me at the time of sale. They also said I could bring it in to get the door aligned but I would have to pay for the repairs.
Furthermore, the truck only came with one key which was a spare key that was programmed to only allow the vehicle to go up 80mph and play the radio at 25% volume. The said they could reprogram the key but it would cost me $200.