Volumetric Efficiency (VE) of an engine is governed by SO many different things. First it is an air pump. Head losses via frictional drag (length and surface roughness) and geometry (turns in the air tract, protrusions) lower the net positive pressure on the intake and raise the net positive pressure on the exhaust. This in turn makes it harder for the engine to breath in and out, lowering VE. That said, the engineers new this and compensated some with valve and ignition timing.

Usually the highest areas of loss are the sharp turns in the intake manifold, overall TB diameter, valve diameters, exhaust system(manifold) turns and sizing, CAT, ETC...
The hype plays to the idea that the most restrictive things are the muffler and your air filter.

The aftermarket gadgets do a little of what the are supposed to. but for the money to HP gain, they are a bust. Particularly if you do ONLY them.

You can Definitely increase the volumetric efficiency of the 4.0. Just starting with the intake, you can build your own manifold with equal length runners of the right harmonic length. Then of course you'd want to increase the size of the TB to make sure it is not the restriction. Now your intake valve/timing is limiting you, and you need to machine the head for a larger valve, or multiple intake valves. While your at it do the exhaust. Of course in order to make sure your not bottle necking at the head you need to enlarge and polish the ports. Next you need to build a harmonically tuned exhaust to fit this hot rod head/intake combo. But now is your bottom end strong enough? How bout light enough? Ok, so you have a great engine that can handle the HP you want, what a bout a fuel delivery system. The stock fuel/ignition curve isn't going to hack it. So you need to dyno tune your new engine. But hey now that a lot of metal is gone from all your machining/tuning, you should probably freshen it up so that you can drive it reliably. Oh hey BTW SMOG...

You see what I'm saying?
The engine is a SYSTEM, and needs to be approached as such. Jeep made a nice strong I6 that last reliably for a long time making some power. In fact it is so well engineered that it will operate outside it's designed parameters and run an exhaust/cat/TB spacer/etc... and make a little(<5%) more HP while still getting an ok mean time between failure.


I don't think the 4.0/5.2/5.9 is, but some are (look at the Mazda CX-7, ~240HP ~250Ft.lb. around 2500 RPM).

I think on a system view a 4.0 can get a better VE, but just cobbling together a bunch of random aftermarket parts and calling yourself a mechanic/engineer is just plain stupid. And for all practical reasons, yeah your just build an engine that will prematurely fail.

And K&N filters are horrible. ESPECIALLY for a jeep. Flow for a given area and a given pressure drop is determined by the diameter of the opening, and roughness of the surface it's touching (first order approximation). A K&N compared to a paper has roughly the same surface area and roughly the same surface texture. So why does one flow better than the other? The size of the openings available for air to flow through. Bigger openings = less flow restriction. The problem for a jeep with bigger openings?? Bigger holes for more dirt to get through! = less life for the engine! If you want HP spend the big bucks and make HP if you want reliability, you already have it!