"I recently bought a Funaro & Camerlengo USRA double sheath Boxcar kit at a show and I have noticed that both ends of the car floor are bent about 0.125" down out of the plane. What is the best way to remedy this situation?"
If all else fails, there's Accurail #105, 40 ft Fishbelly Underframe. You may have to do some adjusting to get it to fit the resin carbody.