Hi otaku. It is a good idea, as you said, to call Ford Motor Credit, or go to the dealer and have them explain the figures to you. Something may be off (it wouldn't be the first time a Dealer tried to "be creative" in their figures) , but then again, it may not be. Assuming I price your car with every option but the NAV and Audiophile (as you state in your other post), you come up with a price of $27,595 MSRP. Not sure where you are located, but I am in New Jersey, so our sales tax is 7%.
$27,595 + $1,931(tax) = $29,526.
Then you subtract $4500 (the $1000 rebate and your $3500 down payment, if you did not include your rebate as part of the down payment), and have a balance of $25,026.
Now you are financing $25,026. I'm not sure what type of financing you received, but taking a worst case scenario of 60 months at 4.9%, your payments would be approximately $471 dollars a month X 60 months = $28,260.
So take the $3500 you put down, plus the $28,260 in payments over the next five years, and you get a total out of pocket of $31,760.
Of course, I am making several assumptions here, such as that you paid about MSRP for the car, 60 months of financing etc. And each one I am wrong about will affect the price one way or another.
Sorry for the long post, but I was trying to be as informative as possible (and hope my math was relatively accurate). Good luck and I hope things work out for the best.