In the end, I just went to the General Manager of the dealership. They took care of it all.
The salesman came and apologized for the miscommunication, and tried to tell me that he didn't offer me any other solutions "because I was so set on the diesel".
FCA did offer to change the engine in the order, but wouldn't be able to do anything about what the cost would be from the dealer. That would have had to be renegotiated.
The only thing strange about my order, was the diesel. So I was able to find what I wanted on the lot. It still took way too long. Ordered in October, order never delivered, countless hours spent emailing, calling, and stopping by the dealership (and FCA); only to spend 6 hours at the dealership on Saturday.
In the end, I feel like I got a good deal. Though, I after putting up with all the crap I did from the salesman, I think it should have been easier and faster to get the deal that I got.