I got tired of trying too find this all the time, written by Speedin Bob.



Intercooler cleaning/Supercharger R&R (LONG post)
Guys,

Listed below are the R&R steps for the removing the Charge Air Cooler (intercooler) per the Ford Service CD. This naturally includes the supercharger assembly. Image inserted where appropriate.

Charge Air Cooler — Lightning


Removal

Item Part Number Description
1 6F076 Supercharger and plenum assembly
2 6F089 Vacuum/actuator/valves
3 9H486 Upper intake manifold gasket
4 9424 Intake manifold
5 9J447 Lower intake manifold gasket
6 6K775 Charge air cooler assembly
7 9461 Lower intake manifold gasket
8 9M436 Charge air cooler gasket

1. CAUTION:
Before any supercharger service, clean areas around the supercharger assembly. Cover the openings of the engine and supercharger while supercharger is removed to prevent damage by foreign material.

Disconnect the battery ground cable. For additional information, refer to «Section 414-01».

2. Remove the air cleaner outlet tube. For additional information, refer to «Air Cleaner Outlet Pipe—Resonator, 4.6L and 5.4L» in this section.

3. Disconnect the throttle position (TP) sensor electrical connector.

4. Disconnect the idle air control electrical connector.

5. Disconnect the vacuum lines and the vent hose.

6. Note:
Pay attention to the throttle return spring orientation. It must be reinstalled in the correct orientation.

Disconnect the throttle control linkages.

Disconnect the speed control actuator cable (9A825).

Disconnect the accelerator cable (9A758).

Remove the throttle return spring from the throttle lever.

7. Remove the three nuts and position the accelerator cable bracket aside.

8. Disconnect the exhaust gas recirculation (EGR) valve.

Disconnect the vacuum line.

Disconnect the EGR valve tube fitting.

9. Disconnect the brake booster vacuum line.

Remove the bracket bolt.

Disconnect the vacuum line.

10. Disconnect the vacuum line.
11. Remove the bolts and remove the throttle body spacer.

Discard the gasket.

12. Remove the accessory drive belt. For additional information, refer to «Section 303-05».

13. Drain the charge air cooling (CAC) system. For additional information, refer to «Section 303-03B».

14. Loosen the CAC hose clamps and remove the hoses.

15. Remove the nuts and position the CAC water supply and return tubes aside.

16. Remove the EGR vacuum regulator bracket.
Remove the nuts.

17. Remove the two upper vacuum hoses from the supercharger bypass valve actuator.

18. Remove the supercharger and plenum assembly.

Remove the bolts.

Remove the stud bolts.

Remove the supercharger and plenum assembly.

Discard the gasket.

19. Remove the upper intake manifold.

Remove the vacuum hose.

Remove the CAC hoses.

Remove the bolts and the upper intake manifold.

Discard the gasket.

20. Remove the CAC.

Remove and discard the bolts.

Remove the CAC.

Discard the gasket.


Installation

1. Note:
New bolts must be used during assembly of the charge air cooler (CAC).

Install the CAC.

Install the CAC.

Install a new gasket.

Install the new bolts.

2. Install the upper intake manifold.

Install the upper intake manifold and the four rear bolts loosely.

Install the CAC hoses.

Install a new gasket.

Install the vacuum hose.

3. Note:
Tighten the retainers in two stages, in the sequence shown.



Install a new gasket and install the supercharger and plenum assembly, bolts, and the stud bolts.

Stage 1: Tighten to 2 Nm (18 lb-in).

Stage 2: Tighten 45 Nm (33 lb-ft).

4. Install the two upper vacuum hoses to the supercharger bypass valve actuator.

5. Install the EGR vacuum regulator bracket and install the nuts.

Position the bracket and install the nuts.

6. Position the CAC water supply and return tubes and install the nuts.

7. Install the CAC hoses and the clamps.

8. Fill the CAC cooling system. For additional information, refer to «Section 303-03B».

9. Install the accessory drive belt. For additional information, refer to «Section 303-05».

10. CAUTION:
The throttle body spacer sealing surfaces are soft metals. Carefully clean both sealing surfaces.

Note:
Inspect the throttle body spacer gasket and install a new gasket if necessary.

Install a new gasket and install the throttle body spacer.

Tighten the bolts in two stages.

Stage 1: Tighten to 10 Nm (89 lb-in).

Stage 2: Tighten an additional 90 degrees.

11. Connect the vacuum lines.

12. Connect the brake booster vacuum line.

Connect the vacuum line.

Install the bracket bolt.

13. Connect the exhaust gas recirculation (EGR) valve.

Connect the vacuum line.

Connect the EGR vacuum tube fitting.

14. Install the accelerator cable bracket and install the three bolts.

15. Note:
Pay attention to the throttle return spring orientation. It must be reinstalled in the correct orientation.

Connect the throttle control linkages.

Connect the speed control actuator cable (9A825).

Connect the accelerator cable (9A758).

Install the throttle return spring to the throttle lever.

16. Connect the vacuum lines and the vent hose.

17. Connect the idle air control electrical connector.

18. Connect the throttle position (TP) sensor electrical connector.

19. Install the air cleaner outlet tube. For additional information, refer to «Air Cleaner Outlet Pipe—Resonator, 4.6L and 5.4L» in this section.

20. Connect the battery ground cable.
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