Again, my focus has shifted away from the 5.4L and to using the new 5.3L stroker shortblock that is based on a 4.6L iron block. This discussion involves '06 and newer Explorers since my vehicle is a 2007 Sport Trac. I also realize I am probably wasting my time trying to explain all that considering current attention spans. LOL! But I do appreciate alternative ideas since it gives myself and others a chance to investigate and dissect those options.
Anyway, what if your engine has high mileage and you are going to need a rebuilt shortblock anyway? Are you going to throw a set of used 4V heads on a high mileage 4.6? Anyone looking for a power increase AND reliability probably wouldn't. Now you have just added the cost of a cylinder head rebuild. How easy is it to mount accessories like the power steering pump, alternator, AC, etc. to the 4V heads? You will also need the 4V intake and exhaust manifolds and probably exhaust system mods to mate up to the 4V heads. Yes, you could probably find a wrecking yard Aviator to rob all that stuff from but I would be hard pressed to recall ever seeing an Aviator on the highway recently let alone in a bone yard. How compatible are all those parts and accessories with a newer Explorer? Can I mount the accessories from my year truck to the Aviator engine? Regardless, I obviously can't use my old intake and exhaust manifolds since they wouldn't fit the 4V heads. Also, will exhaust manifolds from an '03-'05 Aviator even fit inside the frame rails and clear the steering shaft of an '06-'10 Explorer?
A better option might be to find a complete, low mileage Aviator that has been totaled and do a complete swap from that. Not sure what kind of emissions issues you might have to deal with since the Aviator will probably be older than the vehicle you are putting it's engine into. And you still haven't addressed the above issues. No matter how you look at it using 4V heads is probably going to require a lot more modifications to the rest of the vehicle.
My point is that using a brand new 5.3L stroker is probably going to involve a lot less drama and will still result in a decent power increase at lower rpms that should be more usable in a truck. And, by the way, a stock '03-'05 Aviator was rated at 300 lb-ft of torque. Even a stock 3V 4.6L in the Explorer was rated at 315 lb-ft. Most of that power increase can probably be attributed to the variable cam timing (VCT) used on the 3V heads but either way you are going to lose VCT with Aviator 4V heads. My guess is you could probably expect at least 350 lb-ft from a 5.3L with 3V heads. Not sure I see any advantage from 4V Aviator heads. Considering everything necessary to make it work and little, if any, power gains it might even be a step backwards.
If your truck is high mileage you can either have your 3V heads rebuilt or trade them on a rebuilt set. Depending on the year it might be a good idea to upgrade to a set of 3V, 12mm spark plug heads and their spark plug coils to get rid of the older two-piece 16mm plugs in the earlier 3V heads. Everything else should simply bolt on since the 5.3L is based on a 4.6L iron block.