In 2005 I think they moved the APSS to the fuel pedal, in the cab (a good move, in my opinion). Is the throttle connected to the transmission? Or do you mean the kickdown cable?
On edit: I looked over the wiring diagram for the 2006 48RE. I don't see any direct connection to the APPS unit. The TTVA (Transmission Throttle Valve Actuator) is is fully electronic and self-contained, being controlled directly by the ECM.
So the question is, does the ECM on a 2004. 5 truck provide the necessary signals to operate the TTVA? According to the 2004 manual (not sure whether it covers the 2004. 5 trucks or not), the ECM doesn't have the necessary outputs to operate an electronic TTVA. This implies the electronic TTVA from the 2005 transmission would need to be removed, and a cable-operated TTV assembly would have to be retrofitted. Note that all the gas engines use the cable-type TTV (only the diesel uses an electronic TTVA), so it may not be difficult to find a cable one to interchange.
Beware the service manuals warn that the adjustment on the TTV cable is critical, since the throttle valve is the master control for the shifts.
The TTVA is like the electronic shift module on electric-shift transfer cases: it simply actuates the mechanism that's normally actuated by a cable. I'm sure the cable-type system could be easily attached to the transmission after you remove the TTVA.
I've attached a photo of the cable system from the 2006 manual. I hope that helps.
Ryan