The EFI control system will work with any intake.. factory or aftermarket, it's just a matter of connecting all the sensors. The computer is located in the drivers kick panel on the trucks so somewhere like that is where it would have to be in the project vehicle too unless you use a car or aftermarket wiring harness.. which is also possible but requires some pin swapping to make it compatable with the truck computer.
I can also assure you guys the Mustang intake does not flow better than the truck intakes, the 5.8 truck version flows about 30% better and the 5.0 truck version flows close to twice as much air.

The vacuum tree is mounted right on the upper intake on the trucks, and the whole smog system(air pump and attached plumbing and valves) can be deleted without affecting engine operation, just make sure the two control solenoids next to the coil remain connected to the woring harness. The EGR can be disabled but not eliminated, it is a pretty tidy system anyway and actually improves milage so it's worth keeping, but if you don't want to add a connection on headers for the tube simply do as outlined below. Remove the tube connected to the exhaust and put a piece of sheetmetal between the valve and intake but leave the valve connected to it's electrical and vacuum lines. The system will operate normally and keep the check engine light off but it won't pass any exhaust to the intake.