Step 1 is locating a donor vehicle. My donor vehicle was a '92 Explorer 2WD, 4 door automatic. For your engine to function properly, you must consider a few things.  Basically any 4.0 has the same bellhousing as the other ford V6's, and will bolt up to them, HOWEVER, if you are using an automatic,  I highly recommend you take the transmission from your donor vehicle because the older automatics and the newer ones will run and drive together, but it's not very nice. This has to do with the different valve body solenoid setup mainly.  

Take Photos!

**** Be sure you take a picture of the underhood setup before you pull it out!!****

Parts:

Before you select your donor vehicle, you need to know what parts you are going to need which are listed here:

4.0 Engine, complete with all accessories
Throttle cable and cruise control cable/assembly (if desired)
air tube with air filter housing, and Mass Air Flow Sensor
complete wiring harness from under the hood
ECM Computer
wiring harness from A/C Fan
A/C Lines (If A/C is desired)
A/C Condenser (If A/C is desired)
A/C Compressor (Required)
Transmission (Ideally)
Radiator
Motor Mounts (although while it is out is a good time to buy new ones)
Exhaust Crossover Pipe
Catalytic Converter(S)
Fuel Lines
Sending unit/fuel pump assembly (if current motor is carbureted)
Power Distribution box
Charcoal Canister
Inertia Switch
EDIS Module

When you are removing the harnesses from the donor vehicle, DO NOT CUT unless you are 100% positive. It is very nice to have your harness just snap right in.

Great! Now you've got your equipment. Now for the next essentials... Go buy a CHILTON's manual (Not Haynes, their wiring diagrams are poor) for your donor, and for your current vehicles. This will help you figure out where to make certain connections and piece together little bits and pieces (chances are if you get your motor from a wrecker there may be something wrong with it).

Now you're ready to tear in and start your conversion. Pull out your old motor, and trans if you are replacing that too. Strip out all of the old garbage emissions components as well, as the 4.0 setup doesn't require them, and it will free up some space to mount the numerous sensors and modules that go with it.

Fuel System:

If your old setup was carbureted, you'll need to drop the fuel tank, remove the sending unit/pickup assembly and replace it with the fuel injected one. Once this is in place, attach the new fuel lines to it.

Special Recommendation:

Ford didn't make the 4.0 until after 1989, which was when they switched their sending units over to a different OHM range. By installing a newer sending unit in your tank, you will make your gas gauge inoperable. There is a way around the problem, which is also a smart way to go. Get your fuel lines and sending unit from a vehicle like yours. (IE: If you have an '85 Bronco II, find an 86-88 Bronco II and get the sending unit and fuel lines out of it, they are already bent to fit perfectly in your vehicle, and they will work with your factory gas gauge)

Before you bolt the tank back in, ohm out the fuel pump, and sending unit to make sure they are in working condition.

Dropping the motor in:

Replacing the 2.8, you will need to drill new holes for the passenger's side motor mount. I don't remember the exacts of it, but you should eyeball it so it sits level and even with the driver's side one. If you are a little off it won't matter because the mounts are flexible. Drill the necessary holes using your preferred method of locating it, and install it. You should have a bare underhood compartment when you this. Drop the motor in, and bolt it down to the motor mounts. Sit back for a few seconds and admire your beast (well... compared to the previous motor anyway). The motor is done first because it's position is the most important. Your new trans, if an auto, should be the same length as before, and should bolt right in. Put in the trans as you normally would.

Remove the old motor's throttle cable if it won't reach, and install the one from the 4.0. This is also a good time to swap the cruise control  "black box" that connects to the throttle cable, this is just a bolt in replacement for your other cruise control with a different cable, all electrical is the same.

Connect the fuel lines to the engine. I highly recommend you change the fuel filter here, because you don't know what shape the old one is in, and it's cheap as hell.

Electrical Connections:

This is thought to be the most difficult, but actually it isn't.

Retain your original starter solenoid. Locate the power distribution box in the 4.0 harness and bolt it to the battery side of your starter solenoid. It has a short cable, so this should be done first. remove the connections that your original vehicle has there, if any. Now it is time to start soldering. Your new Power Distribution box  has a provision for an ignition switch. cut off the ring terminals from the wires that were connected to the battery side of the solenoid and solder them onto that. It has a 60 amp fuse on the circuit which is plenty.

Locate your original ECM and remove it, and the harness that went with it. Run the 4.0 harness in through the hole in the firewall and hook up the ECM to it. Go through and plug in all the connectors that you removed in the process, and put it back together the way it was, so basically what you will have under the hood is a complete 4.0 system as it was in your donor vehicle, and I will guide you through integrating this newer system to the controls of your older one.

First, we will do the starter. Locate the starting/ignition diagram in your repair manuals for each vehicle, and splice the appropriate wires together over on the firewall on the driver's side. In my case, it was a Red/Blue wire going to a Pink wire in the 4.0 harness. Then take that over to your solenoid to the "S" terminal. Then you will need to take some light gauge wire from the "I" terminal and run it down to the heavy duty starter cable. Connect that wire to the solenoid that is on the starter itself, and connect the heavy duty cable in the obvious place. At this point, you should have power to crank your vehicle over from your ignition switch.

Now we will supply fuel and power to the engine so it can start. Start with the Fuel Pump.

The #1 fuse in the power distribution box is a 30 amp fuse for the fuel pump. There is a connection in the 4.0 harness that runs all the way back to the fuel pump, and the inertia switch comes in the cab where the computer and blower motor wires do. Connect the inertia switch, and mount it anywhere up under the dash there, being sure the red button is facing up. Run the wires back on your frame rail back to the fuel pump connector, and connect the other end to the appropriate connector near the firewall on the Driver's side. Now locate a red/green wire in both harnesses here. Solder those together and this powers everything in the 4.0 harness. After connecting all appropriate connectors, and GROUNDS, DON'T FORGET GROUNDS, Turn your key to the on position. If you hear the fuel pump engage in the tank, you should be able to turn your key and start the engine, because the ECM power relay turns on the fuel pump relay and the power to your Distributorless ignition.

Next we will connect your alternator. The field terminal on the alternator runs to your power distribution box, and the power cable connects to the battery side of your starter solenoid.

Your oil Pressure and Temperature gauges will connect and work with the 4.0 sending units. Connect them on the firewall on the driver's side.

Your ECM requires an input from your brake light switch in order to control the transmission properly. It connects to Pin 2 which is a light green wire. Locate the side of your brake switch that DOES NOT have constant power and tap onto it with this wire. (this will alert your transmission to disengage the TCC Lockup and also come out of overdrive).

The Fuel Gauge will work if you used the proper OHM range sending unit, otherwise you will need to install an aftermarket one, which is what I did. This will get you running and on the road.