I agree that the fender sounds like damage at the dealership and wasn't disclosed to you upfront.
I think everyone is mistaken on the "rebuilt transmission" statement. I don't think the dealer wants to put a rebuilt transmission. What he means is to rebuild the one he already has. Probably faster to rebuild his than try to get a new one from FORD. I agree I don't like this option either but this is what they do all the time.
I had a brand new 91 Accord and the stock fancy Alpine cassette player went out after 3 months of ownership and Honda could only offer me a refurbished radio/cassette player. On a brand new car! That really pissed me off. Never bought another Honda after that!