I have a 2003 f150 w triton 5.4 engine, automatic trans 2WD, am replacing bad tranny w one from 2003 f150 but with 4.6 engine, and wiring harness for the new one,(4.6), has 3 connectors where mine only has 2. What is this 3rd and how can I make it work?

 

The trans with the 3rd plug, input speed sensor, is a 2004-up trans. It will not work as the output speed sensor pickup in the trans is different, up to 2003 it read off of holes in the rear ring gear, 2004-up, it read off the park lugs on the ring gear.