To start, while not impossible, a 4.6 is a very tight fit in that engine bay. That is why the Explorer kept the 5.0 longer than any other vehicle. Be prepared to potentially lose your A/C. A body lift will probably help.
Anything can be lined up with anything else. That's not hard. A 4.6L engine will not mate up to a 3.0 transmission. The bell bolt pattern it wrong, I think the 4.6 flex plate won't even fit inside the bell, and the engine would probably shred that transmission.
Cost is hard to estimate. Each swap is different, and parts availability and prices will vary by location. Also, the 4.6 swap isn't as well documented as the 5.0 swap.
You will, at least, need an engine, trans, wiring, computer, and exhaust. You will likely have to do something custom with the steering, and as said before a body lift will probably make things less painful.
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