Swapping 4spd for 5spd Auto transmission?

Not sure where you found a 5-speed automatic. Ford had the 4-speed automatic version of the AOD in the F15o until they introduced the 6-speed automatic in 2009. The 6-speed cannot be swapped into the earlier trucks without changing most of the wiring harness and many of the powertrain control system modules. That is because it has sensors and controls that the 04 doesn't have the wiring or ability to control.
Now if you were thinking of the 5-speed manual transmission. That could be swapped into your 2004 but again it requires multiple changes for it to work properly. A different PCM, BCM and different supports for the pedal assembly to add a clutch pedal and modifying the floor for the shift assembly. Plus, the transmission wiring harness is different as is the GEM programming. Once the computers got involved the old ideas of simply swapping things around really got turned on their heads. These days it's almost always a better idea to go find the vehicle built the way you want it and sell the one you don't.