3 of the wires are as you would think, a convential potentiometer, The other 3 wires are 2 calibrated position switches, Used for idle validation..IE "idle" and "not idle" , these are for lack of a better term and to keep me from typing a book, watch dogs, in the event of a failure and/or erroneous signal from the position sense to tell the ECU that "hey...the pedal is at idle" so it won`t run away.
Eric You really need to get some sort of scan tool if you don`t have it so you can access the data stream...NOT one of those freeking code readers, you really need to see if the ECU and the FPCM (electronics in the pump) are talking to each other, it will aid greatly in diagnosing such an unknown.
Few know that you can creativly toss 12 volts at a VP with nothing else hooked to it and get it to start and idle, Plus while there is a good possibility that the APPS may be an issue, ALOT of VP "dead pedal" issues stem from the pump electronics itself, especially with 98.5 and 99 model years and without being able to at least access diagnostic codes and data you are shooting blind with expensive parts.
Contrary to "internet" opinon lift pump pressure at this point is a wasted thought, the vane pump in a VP is capable of drawing fuel on it`s own and it will still take throttle, while it won`t be happy for long like that it will run

Just 2 more cents worth

Rick