IMO the chassis is pretty stiff, try driving with the windows down and the radio up and see how it "feels". When you can't hear all the noise inside the car it makes a big difference in perception.
That said, the problem is really the choice of materials Ford used for the interior of our cars (cheap CREAKY plastics) that are far too responsive to vibration and temperature changes (ever notice that some noises come and go with the weather?
)
Two things I have done to reduce noise are 1) take the rear seats apart and spray all the vynil/leather edges with silicone, as well as the edges of the front seats where they rub against the doors and console. Then 2) Wrap the spare tire jack and iron with some cloth and MAKE SURE THEY ARE TIGHT. If the tire and jack arent tight they will make ALOT of noise.
Eventually I'll try doing
warmonger's method to remove noise from the doors. 
