Based on the info in the manual, the VSS must be used during warm up for something. Why would a cold engine running between 2000 and 5000 rpm need to know the truck speed, except when racing the engine? Maybe some sort of deceleration control for emissions like the old throttle positioner...
I read the brochure on the GPS unit. It outputs a sine wave or square wave Pulses Per Mile (PPM) signal. The 3fe ECM is looking for a reed switch opening and closing in proportion to vehicle speed so it can make it's own pulses. I am not sure any of the outputs from the DD GPS unit will work...