I put the procedure I used in text format. I started with a procedure that someone else posted for a 98 which also included replacement of the coolant tube in the engine valley. This procedure should give you an idea of what all it entails. I agree with the other posters. Take your time and do it right otherwise it'll wind up costing you a lot more (like it did me).
1999-2001 Mustang - KIT- 1R3Z-9424-AAA
1W7Z-9424-AA Intake Manifold (1)
1R3Z-10153-AA Alternator Brace (1)
W708309-S437 Water Outlet Connection Bolts (2)
YL3Z-9439-BA Intake Manifold Gasket (2)
F1VY-8255-AA O-Ring For Thermostat (1)
2R33-12B637-AD Wiring Harness (1)
SK 1W7E-9E473-BA Instruction Sheet (1)
Bought 180 degree thermostat (stock is 192 degree) from AutoZone
Bought thermostat O-ring for $5.00 from AutoZone
1.Relieve fuel system pressure
a.In the trunk, unplug the inertia switch electrical connector from the bottom of the fuel pump switch
b.Start the engine and allow it to run until it stops. This make take a few seconds or up to 10 minutes.
c.The fuel system pressure is now relieved.
d.Reconnect the connector to the bottom of the fuel pump switch.
e.If the inertia switch was “popped” on the fuel pump switch then push the reset button on the top of the fuel pump switch.
2.Disconnect cable from the negative battery terminal (8mm)
3.Remove serpentine belt (place 1/4” drive extension in tension pulley and turn clockwise)
4.Remove air inlet tube
a.Unplug the connector at the MAF (mass air flow sensor)
b.Unplug the connector at the IAT (intake air temp sensor) located directly upstream from the MAF
c.Unlatch the connector holding the air inlet tube to the air cleaner housing
d.Loosen the hose clamp holding the air inlet tube to the throttle bottle
e.Disconnect the two PCV (positive crankcase ventilation) tubes coming off of the air inlet tube
i.Disconnect the one from the intake plenum
ii.Disconnect the one from the drivers side valve cover and turn the elbow down to prevent anything (fuel or coolant) from going down it
f.Remove the air inlet tube. The rubber might be stuck on the throttle body opening, gently nudge it off.
5.Remove the alternator
a.Disconnect the 2 electrical connections at the back of the alternator. The nut under the red cap is 11mm.
b.Remove the 2 lower alternator mounting bolts (10mm)
c.Remove the 2 upper alternator mounting bolts (10mm)
d.Remove the 2 bolts connecting the alternator bracket to the intake manifold (10mm)
6.Remove the bolts retaining the alternator bracket to the intake manifold
7.Remove the intake plenum
a.Remove the 2 electrical connectors (2) from the plenum (p-side)
i.Throttle positioner
ii.Idle speed control solenoid
b.Remove red vacuum line from the plenum, EGR, d-side fuel rail, and bracket at back of manifold (green line should be on top)
c.Remove PCV connection from front of plenum and swing the hose out of the way
d.Unbolt the bracket holding the accelerator cable and speed control cable (10mm)
e.Remove accelerator cable, speed control cable, and spring from the throttle body
f.Remove EGR (exhaust gas recirculation) bolts from d-side of plenum (10mm, longer bolt on right)
g.Disconnect the hose from the back of the plenum
h.Remove the 5 bolts holding down the plenum (10mm)
i.Remove the plenum/throttle body
8.Remove electrical connections from the fuel injectors and ignition coils
9.Disconnect ignition wire brackets, boots, and wires and set them out of the way
10.Disconnect the electrical connectors from the Coolant Temperature Sending (CTS) unit (front of p-side of manifold)
11.Unbolt the fuel rails themselves. These are held in with 2-8mm bolts each. You will need a deep socket to reach the nut itself though. (HINT: Beware of fuel spill!!! There is still a little fuel in the lines)
12.When you go to remove the fuel rail and its rubber white lines, the injectors will seem stuck. They are just held in by o-rings, and will “snap” out of place.
13.Remove the injectors and place into the new intake manifold
14.Move the fuel rails up and back out of the way.
15.Drain coolant. Place a bucket under the radiator drain fitting located at the lower corner (p-side) of the radiator. Loosen the fitting, use a 3/8 hose to direct the coolant into the bucket.
16.Remove the thermostat housing bolts (10mm). Move the hose and thermostat housing out of the way.
17.Take the thermostat out and place in a clean safe place. Replace the o-ring with a new one.
18.Unbolt the intake manifold. It is held on with 9-10mm bolts. Remove manifold and place to the side.
19.Remove the intake manifold gaskets. Clean the surfaces thoroughly. Do not scrape aggressively or you’ll scrape up the surface.
20.One area of concern is with the sealing of the intake to head. Inspect the areas of sealing, and if there is any concern, use some RTV gasket maker in those spots.
21.Take the passenger side CTS and apply new Teflon tape to the threads. Replace it into the threaded spot on the intake manifold.
22. Install the new intake manifold gaskets. Both sides are identical. Make sure the tabs face down.
**** VISUALLY INSPECT EACH INTAKE AND EXHAUST PORT WITH A FLASHLIGHT TO MAKE SURE NOTHING FELL IN THEM
**** OTHERWISE, YOU'LL BE FIXING OR REPLACING A HEAD SOON AFTER BUTTONING EVERYTHING BACK UP
23. Install the new intake manifold. Torque specs are 22-31lb-ft of torque. There is a specific sequence, so refer to a repair manual (like Hayes) for the diagram showing the sequence.
24. From here on out, its pretty much reverse of what was done above. Here’s a few tips:
a.Put a dab of oil on the injector o-rings before re-installation. This will help make sure a solid seal is created.
b.When starting the car back up with the coolant back in the motor, and everything tightened up, it will run rough for a couple minutes. This is completely normal and will go away when the computer gets its parameters straight.
c. Don't forget to RTV the coolant port on the back of the driver side head. When I did the front passenger side head I assumed I was done because the front driver side head was a perfect match to the gasket. I forgot that these heads are interchangable between the pass side to the driver side.
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