I am not a 4.0L Tech so I could be wrong but an internal combustion engine is nothing but an air pump; more in / more out, it is that easy !
Some motors will respond to modifications more than other but basic increases in the air in and out theory should result in gains in either torque or horse power.
When you talk increasing the air flow through the motor you will need to address the Camshaft also.
Add more air at the intake without corresponding increases in valve lift and duration and you will not see much increase.
Headers are the one thing on most engines that are restrictive enough in OEM Form so when you change to a tubular header you will see some response. How much hard to say, but you will notice the most change in HP and Torque IF you air more air in and change the cam too.
One way to make a difference in the cam lift/duration instead of changing the cam is to increasing the rocker arm ratio of the OEM Rocker Arms, adding a Roller Rocker at the same time deceases friction.
Go from say a 1.6 to a 1.7 Rocker Ratio and you effectively increase the lift of the cam which in theory should increase the torque for a seat of the pant type of response and may help on the top end HP too.
How a 4.0L will respond to these mods, IMHO… if you do all three, Intake, Cam/rockers and headers, the engine has to make more power, how much I can’t say.
p.s. Don’t forget to alter the chip or add a power chip to compensate for the extra air going through the engine.
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