Engine removal tips:
The engine will come out, and that is the easy part. It becomes obvious if you need to disconnect or move something. Putting it back together three weeks or three months later is a different story. You will have forgotten many small but important details.
A word of wisdom: tag every wire you disconnect and tag the place you disconnected it from with an identical tag. If you take the time to note the wire colors on the tags for the body mounted items, it will be a foolproof method of keeping track of what plugs into what. Number the tags so that you know if one is missing. Do the same thing for the vacuum lines.
Put all the bolts from each item you remove (starter, alternator, smog pump, etc.) in a separate zip bag and put a piece of paper inside the bag with the number of bolts, their sizes and the item they went to. Then you can throw the zip bagged bolts in a 5 gallon plastic pail and still keep up with them. Zip bag each of the small items and put a piece of paper inside identifying the item and where it goes.
Some removal tips...
Unbolt the headers from the engine, but keep the funny looking plates bolted to the head exhaust flanges. They are useful as lifting ears to attach the hoist chain.
Do not use bolts threaded into the aluminum intake manifold to lift the engine
You will need to disconnect the headers from the H pipe and the H pipe from the mufflers. This will be one of your big challenges. The bolts are usually rusted enough to require application of PB Blaster and extreme force. Soak the bolts with PB Blaster and let them sit overnight if possible. Buy a thick walled 6 point socket to attack the header and H pipe bolts. Depending on who was the last person to remove the nuts and bolts, they are either 11/16" or 5/8" heads. Be prepared to apply a propane torch to the nuts if they threaten to round off even with a 6 point socket.
Disconnect the negative battery cable. This will prevent sparks and short circuit damage if you ground out something electrical while removing it.
Put a 2x4 wood block under the engine oil pan to support the engine. Jack it up slightly. This prevents damage to the motor mounts when the transmission mount is removed. The oil pan is plenty strong for this purpose. Disconnect the negative battery cable. Label all the wiring for the transmission before disconnecting it. Disconnect the O2 sensor cables at their connectors. Disconnect the speedo cable by pulling it straight out of the VSS sensor, or by removing the bolt that holds the VSS sensor in place. If you remove the VSS sensor, zip bag & tag it along with the bolt that secures in place.
5 speed transmission cars:
Put a catch pan under the rear of the transmission to catch the fluid when you slide the yoke out of the transmission. I recommend that you drain the transmission at this time. There is a pair of pipe plug filler ports on the side of the transmission. Use the lower plug to drain the fluid.
Inside the car, remove the shifter boot and then remove the shifter handle
Remove the H pipe & rear trans cross member. The chassis to cross member bolts are metric, you need a 15 MM & 17 MM socket or wrench. Note the direction and size of the humps on the cross member and write it down. Inspect the rear transmission mount and replace if damaged.
See the following website for some help from Tmoss (diagram designer) & Stang&2Birds (website host) for help on 86-95 5.0 Mustang wiring
Mustang FAQ - Engine Information Everyone should bookmark this site.
Ignition switch wiring
http://www.veryuseful.com/mustang/tech/engine/images/IgnitionSwitchWiring.gif
Fuel, alternator, A/C and ignition wiring
http://www.veryuseful.com/mustang/tech/engine/images/fuel-alt-links-ign-ac.gif
Complete computer, actuator & sensor wiring diagram for 88-91 5.0 Mass Air Mustangs
http://www.veryuseful.com/mustang/tech/engine/images/88-91_5.0_EEC_Wiring_Diagram.gif
Complete computer, actuator & sensor wiring diagram for 91-93 5.0 Mass Air Mustangs
http://www.veryuseful.com/mustang/tech/engine/images/91-93_5.0_EEC_Wiring_Diagram.gif
Complete computer, actuator & sensor wiring diagram for 94-95 5.0 Mass Air Mustangs
http://www.veryuseful.com/mustang/tech/engine/images/94-95_5.0_EEC_Wiring_Diagram.gif
Vacuum diagram 89-93 Mustangs
http://www.veryuseful.com/mustang/tech/engine/images/mustangFoxFordVacuumDiagram.jpg
Vacuum Diagram 87-93 Mustangs
The diagram says 88 Mustang, but except for the vacuum line connected to the MAP/Baro sensor, it is the same for all 5.0 Mustangs from 87-93. The 89-93 Mustangs vent the MAP/Baro sensor to open air.
http://www.veryuseful.com/mustang/tech/engine/images/88Stang5.0Vacuum.gif
HVAC vacuum diagram
http://www.veryuseful.com/mustang/tech/engine/images/Mustang_AC_heat_vacuum_controls.gif
TFI module differences & pinout
http://www.veryuseful.com/mustang/tech/engine/images/TFI_5.0_comparison.gif
Fuse box layout
http://www.veryuseful.com/mustang/tech/engine/images/MustangFuseBox.gif