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You will find an ignition coil on top of each spark plug. On a Ford 5.4L, the injectors and coil-on-plugs are right next to each other. Coil "D" is located at hole #4, which is the rearmost hole on the passenger bank.
The arrangement looks like this:
******firewall
4 8
3 7
2 6
1 5
******nose
where #4 is coil "d"
You will need to remove the fuel rail to remove this or any coil on the engine. Try unplugging your coils one by one, one at a time. Whichever coil you unplug that doesn't make the motor run any worse is the culprit. I think you'll find it on the passenger rear hole if you are looking for coil d.
I just finished replacing the coil-on-plug (COP) ignition assembly for cylinder #4, on a 5.4L V8 installed in a 1999 Ford Expedition. The removal of the fuel rail is not necessary. I was able to remove the COP without removal of the fuel rail. You will need to temporarily move rubber heater hoses out of the way - this can be accomplished by using bungee cords, so that you can get access to #4 cylinder. And you'll need to disconnect the electrical fitting on the fuel injector immediately adjacent to #4 cylinder so that you have enough room to remove the COP assembly from #4 cylinder.
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