Have you inspected the wiring for the fuel injectors and the coil packs for the side with the misfires? Sounds like something happened to the wiring to cause only one whole side of the engine to run like crap. There's no way that every one of the lifters failed to pump up at once unless the whole head is just caked with sludge. They are VERY easy to pull the valve covers... I think the gaskets are even reusable.
It has a 4.7L right?
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