Hello out there in internet land!

I have a question about fuel economy and my 2015 diesel f-250. When I bought the truck, I didn't know it had an aftermarket air intake and some sort of aftermarket exhaust. On my way to pickup some goats in california (towing a livestock trailer) I was getting 12 MPG. What im wondering is if its possible these modifications are impacting my fuel economy and if I should have the dealer put i back to a stock confiuration? I will also add that the air intake (I thinks its a K&N its seems quite big) cause a hole in the secondary cooling hose that I had to get fixed which cost about a thousand dollars

Any help you could provide would be much appreciated.

 

What's the weight of the loaded trailer? And/or weight of any bed load and passengers etc.