Are you running a super charger?
are you sure you're not over thinking this? Without going back through this thread to see what you are trying to do let me say the best air intake system for a mild street build is the stock air box with a
k&n filter.
i will call bull on the 5* difference between the engine compartment and the cavity inside the fender when the car is in motion, maybe setting in traffic at a light with extended idle time the temp between the two can get close to the same. It also is dependent on filter container too, if you look at the pic of the air box on the facepage you posted I bet it is thin plastic which offers no heat insulation at all where as the stock air box is a thicker fiber type material. You could also wrap the pipes between the air box- to maf and the maf to tb with something like dynomat to lower the intake temp, in reality you will not notice a difference unless your engine compartment is on fire.
Once again this is just the ramblings of a back yard hot rodder and in no way an example of any real mechanical training.
Here is an example of 'why did they change that and what is the difference ', the 5.0 ho engine in the fox mustang has the act sensor (air intake temp sensor) in the lower intake manifold but the 5.0 ho in the explorer placed it in the air box.