The 96 Explorer EGR works the same as the 86-93 Fox 5.0 Mustangs.
The Explorer intake manifold vacuum routing is a little different, but not difficult to manage. The Explorer intake swap tech note below will help you get things working..
Explorer intake swap.
The ACT (Air Charge Temp) sensor will probably need to be moved. The early Explorer/GT 40 lower manifold isn't drilled & tapped for it to go into the intake like the stock manifold was. There is a boss cast into the early Explorer/GT 40 lower intake manifold, but a machine shop will have to drill & tap it. Use a 37/64" drill and 3/8 " pipe tap for the ACT sensor. 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".
Use the TPS and IAB from your old throttle body. All the EGR passages were there and fit OK. Use you old fuel rails and regulator. You will probably need a new EGR spacer adapter and gaskets. Without the EGR spacer, there is no place to mount the throttle linkage support bracket.
I used the stock water lines on the Explorer manifold and they connected up to the EGR without any problems. I made a “U” out of ½” copper pipe and sweat soldered it together. Then I used it and some hose with clamps to bypass the leaky heater.
The vacuum lines you need are 1 small line for fuel pressure regulator, 1 small line for A/C,1 small line for EGR and another small line for the smog pump. One big line at the back goes to the vacuum tree for the power brake & A/C, one big line goes to the PVC valve. The other big line goes out the front for the carbon canister. In a pinch, one of the small lines can connect to the spare port on the vacuum tree. Cap or plug the remaining lines since they aren't needed.
The stock Explorer linkage didn't come anywhere near fitting, so I made an adapter plate for the throttle linkage so I could use the 65 MM throttle body.
This is what I did:
Make a drawing of the position of the old throttle body linkage arm and its angular position relative to the centerline of the throttle body. Remove the ball stud off the explorer TB to make way for the adapter plate. Drill and tap a 10-32 hole in the linkage parallel to the TB shaft. Make an angle bracket out of 1" angle iron 3/8", drill a 3/16” hole in the center of each one of the legs. Then bolt it on where the hole was drilled & tapped. Then make a circular adapter plate out of 1/4" thick aluminum to bolt the two linkage arms together. Then bolt the aluminum plate to the existing linkage, and the angle bracket. Next mount the arm with the ball stud off the old throttle body on the adapter plate using the drawing to get the angle correct. You will need an aircraft type countersink for one of the bolts that secures the plate to the explorer linkage arm. It ends up being under the arm with the ball stud for the linkage. It works great and looks neat.
The Explorer TB could have been real simple if I had a gas welding torch or taken the TB to a welding shop. Just grind the mushroomed part of the TB shafts so that you can pry the linkage arms off. Then swap the stock arm onto the Explorer TB and braze it onto the shaft. It Takes about 3 minutes or less worth of work with the torch, so it shouldn't cost much.
I didn't have access to a welder, so I fabb'ed the plate in my shop. I took about 1.5 hours to do it, it was a measure, cut, and fit type of operation.
Also see http://www.veryuseful.com/mustang/tech/engine/ConvertingExplorer65mmTB.pdf
for modifications to adapt the 65 MM Explorer TB to a Mustang
Vacuum line connections:
One large vacuum line from the upper front goes to the carbon canister
One large vacuum line from the rear goes to the vacuum tree.
One small line in the front feeds the Smog pump solenoid control valves on the rear of the passenger side wheel well..
One small line in the rear goes to the fuel pressure regulator.
One small line in the rear goes to the EGR suction regulator.
One large line in the rear goes to the PVC valve.
Diagram courtesy of Tmoss & Stang&2birds - Typical Vacuum Routing for a Fox stang 5.0: