The spark plugs are located below the 'coil pack' in a hollow tube in the head. You must remove the spark coil retaining screw to access the removal of the soark coil. The reoval with expose the spark plug at the bottom of the hollow tube in the head. The total spark coil is about 6-7" long and when it comes out that is when you will see the spark plug at the bottom of that tube. It sounds difficult to find but once you know it is easy. There is no coil wire(typical spark plug wire) attached to the spark coil. It is fed by a special connector on the side of the spark coil. Look on the side that has the least number of hoses and equipment in the way. Find the top of the spark coil (about 1-3/4-2" in dia) with a wire connected on the side. There is a single small metric bolt holding the spark coil in place. It will not come out until that screw is removed. I hope that this helps.
They are in the center top of the engine. The plenum has to be removed in order to gain access.
SOURCE: changing spark plugs
Changing the spark plugs on a 1997 Ford Expedition 5.4L engine takes patience. Remember to start this project on a cold engine! I started on the passenger side by locating the Coil over iginition coils and cleaned out all the old dirt using some compressed air. Then I had to disconnect the electrical connections to both the Coil over ignition coils and the passenger side fuel injectors. Once you remove the small bolt which holds the ignition coil in place, use your compressed air again to blow out the spark plug hole. After that, you will need a 5/8" swivel spark plug socket and various length extensions to remove the spark plugs. Take your time because there is not much room for your hands. Before installing the new plug, check the gap and use clean engine oil on the new threads. Tighten the new spark plug and reinstall the coil over ignition coil. Reconnect the electrical connection to both the ignition coil and the fuel injector. Continue these steps with all eight spark plugs. You will find the ones on the drivers side are difficult because of the fuel rail gets in your way. Have patience and use swivel extensions to work around the tight spaces. When you are done, you will have saved lots of money! Don't forget to replace your air filter, fuel filter, and pcv valve to complete your tune up.
SOURCE: 2001 ford expedition spark plug location
That's because they are hidden quite well. If you look at the engine, you'll see yellow plastic prongs (?) that look like spark plugs, but hook up to the silver tubing. That's the fuel injectors. BUT, right behind the yellow plugs, are black ones. The black one is the connector to the spark plug. The plug itself sits about 4 inches down into the block of the engine. They are a real pain, and from what I can tell, you only have decent access to the first 2-4 of them, then they get too far back and start going under the dash (you'll see what I mean when you get there).
SOURCE: removed spark plug wirers need firing order Ford Expedition 1999
Several engine sizes there...
1999 Ford Expedition 4.6 liter SOHC V-8 VIN "6" 
1999 Ford Expedition 4.6 liter SOHC V-8 VIN "W"
1999 Ford Expedition 5.4 liter SOHC V-8 VIN "L"
Hope this help to solve it (remmeber comment and rated this).
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