This is part of a tech note I wrote for a Explorer/GT40 manifold swap. It details the fix for your problem.
The ACT (Air Charge Temp) sensor will probably need to be moved. The manifold isn't drilled & tapped for it to go into the intake like the stock manifold was. There is a boss cast into the manifold, but a machine shop will have to drill & tap the new manifold. The best spot for the ACT is the air box if you don't do the drill and tap thing. You get to cut and splice the 2 ACT wires in order to make them long enough to reach the air box. Solder the wire extensions on the existing wires & use heat shrink tubing to cover the splices. Offset the place where you cut the wires so that you don't have a big bulge when you put heat shrink over the 2 wires to cover & protect them. The air box gets a hole (5/8" or so) for the ACT drilled about 1 1/4" down & 1/1/4" in on the front top side near the upper radiator hose. A brass fitting nut from Home Depot or Ace Hardware secures the ACT into the air box.
If you are very clever, you will find that the ACT connector comes apart so that you can remove the pins. A very small screwdriver releases the lock in the front of the center insert, while another small screwdriver inserted in the back pushes it out. Once the center insert is out of the connector shell, the pins come out easily. New pins are available from AutoZone in a $5 electrical pin kit for Fords. Crimping the pins on the extender wires saves you from having to splice them twice: once to put the connector on and once to extend the wires.
6 ft black 18 gauge wire
6 ft green 18 gauge wire
6 ft 1/4" heat shrink tubing
1 ft 3/16" heat shrink tubing
Measure the 2 extender wires & cut them to length, crimp one set of pins on them. Then mate up the extender pins with the wiring harness & slide the 3/16" heat shrink tubing over them & shrink the tubing. Then slide the 1/4" heat shrink tubing over the pair of wires and shrink the tubing. When you are done you'll have about 1" of wire left without heat shrink tubing on it to strip & crimp the new pins on. Stick the new pins in the old connector shell, assemble it and you are done. It looks as good as factory. Some wire loom can be used to enhance the "Factory Look".