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Hello,
It is right behind the airbox.
Smoke test and watch around the intake manifold gasket.
Before replacing more parts, like the ICM, remember that misfires can occur due to fuel, air, spark, or compression issues.
Be happy to help with this problem - however you're going to need to get the trouble code numbers read and post those numbers here for more help.
The code numbers will tell us which cylinder is misfiring - also if the problem is in the primary circuit (going 'to' the coil) - or possibly in the secondary circuit (defective coil) .. Once we have identified the actual cylinder(s) that's causing the problem - diagnoses becomes a LOT easier.
Side note: The intake manifold issue on the 4.6 liter was coolant leak related due to a split in the composite material at the thermostat housing area. I'm not aware of a vacuum leak from the intake that would cause a running condition concern. I would lean towards secondary ignition issues - or a cracked spark plug. I've had trouble with "aftermarket" coils by the way, I lean towards using Motorcraft coils.
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Where? on the driver side fender?
You know what, I was looking under the wrong car. The engine control module on that vehicle replaces the ignition control module. The camshaft sensor and the crankshaft sensor report their position at all times, and the engine control module tells the coils when to fire. But, really, the 4.6 liter is notorious for intake manifold leaks.