Door fell off hinge pins during reinstall

I enjoyed having the doors/top off my Badlands all summer long. I went to put my doors back on and ran in to an issue. Driver side door went on just fine. The passenger side door was another story. No matter how much I tried I could not get the door to sink fully in to the hinge pins. I tried for hours and even had someone else come over to help out but could not get it as well. The top hinge will rest on the pin but will not fully seat downward. At one point I thought it had gotten enough on the pin to be stable and when I went to reach for the bolt the door fell off the hinge and hit the corner on the ground. I had blankets on the ground, but it still bent the corner of the door pretty badly. Now the door won't shut at all. I took it to the dealer the next day and they had trouble getting the door on as well. Eventually we were able to get the bolt to catch the thread and we had to tighten the bolt enough to force the door to sink down on the hinge pin. I asked if it could be fixed and they told me to take it to a body shop and said the dealer could not do anything and warranty wouldn't cover it. I took it to a Ford body shop the next day and they're less than helpful. They don't believe me and they think I backed in to something with the door open. They are trying to tell me that the hinge pins should be fine since "if the door came off then it should go back on just fine." They are trying to charge me almost $2000 to have the dent repaired.

What are my options? Will Ford cover any of this? Do I need to go back to the dealership? I'm concerned that something happened at the factory during assembly and they had to basically force the door on the hinge pins like I had to do at the dealership. How do I reach out to Ford about this issue? Any one else run in to this while trying to get the doors back on?