^Ignore that comment, you don't have any speedometer drive gear.
Welcome to The Ranger Station!
Please tell us more about your vehicle:
I'm ASSuming you have a 4WD since you swapped in an Explorer drivetrain.
Read this link:
http://www.therangerstation.com/tech_library/speedometer.shtml
I can only GUESS that the 99 Donor used the VSS from the rear axle for its speedometer. Since I ASSume that you installed the SOHC's PCM and engine bay wiring, it should receive the raw VSS signal from the rear axle straight to the 4WABS Module. The 4WABS Module puts out the VSS signal on the Gray wire with a Black stripe (Gy/Bk). It then goes to Sppedo, Cruise, GEM and PCM.
Your old 2001 3.0 Automatic MIGHT have used a VSS from the transfer case or the tailshaft of the automatic trans. I DON'T KNOW. I do think you should figure out how the Donor's speedometer worked (My ASSumption may be correct) and you absolutely have to find out how your 2001 speedometer got its signal (which I think is different).
Worst case, you'll have to scab in a 4WABS module to condition your raw VSS signal. You won't have to PLUMB it, but it'll have to be electrically connected.
You might get some Donor information from
http://www.explorerforum.com/forums/showthread.php?t=336871&highlight=speedometer
http://www.explorerforum.com/forums/showthread.php?t=266929&highlight=speedometer
http://www.explorerforum.com/forums/showthread.php?t=176449&highlight=speedometer
"To answer BB's question though, on a 99, the speed sensor on the rear axle is one of three inputs into the ABS Control Module. The ABSCM conditions the three signals, then outputs the vehicle speed as an input to a whole assortment of things, including the speedo, trip computer, ECU, PCM, GEM, Cruise Control Servo, Stereo, and a few others I'm sure I forgot. If one of the ABS sensors drops out, the ABSCM still has the other two to rely on to determine vehicle speed." <That describes your Donor.