Intake

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The stock intake system of the 5.0L V8 is highly restrictive so opening up this side of the engine to improve its ability to breathe in is the first step towards increasing its volumetric efficiency. The easiest approach to modifying the intake system on a stock 5.0 engine is to replace everything upstream of the intake manifold (air filter assembly, MAF sensor housing, airtube, and throttle body).
The stock intake manifold is also restrictive at higher rpm but since a performance intake manifold should be matched to the cylinder heads and camshaft, intake manifold swaps are often performed together with the heads and cam (collectively known as the H/C/I). Indeed you can buy these as matched components in the Trick Flow, Holley Systemax, and Edelbrock upper engine kits.
While it is necessary to get more air (and fuel) into the engine to improve its performance, that air must be as cool as possible (cool air contains more oxygen molecules) in order to derive the best performance gain (each 11*F increase in intake air temperature results in a 1% HP/TQ loss). While installing an air filter assembly that draws cooler air from the passenger side fenderwell is a step in the right direction, the stock intake manifold (and the air inside it) becomes very hot because it conducts heat from the cylinder heads. The upper intake manifold temperature can be reduced dramatically by installing a phenolic spacer between the upper and lower intake manifolds. This simple, inexpensive bolt-on modification not only increases the mass flow of the air entering the engine, but cooler air also reduces the engine's tendency to detonate thus allowing more ignition timing advance for further performance gains. This excellent tech article by Autospeed explains in more detail how intake manifold spacers work:

Cool Stuff - Manifold Insulators

Since the spacer increases the intake manifold runner length, it also produces a small gain in torque at low/medium engine speeds and shifts the torque peak to slightly lower rpm.

C&L 76mm MAF Kit

The stock MAF sensor housing has a 72mm bore but a 19mm wide bar runs down the middle causing a major obstruction to airflow. The cross-sectional area is a mere 27.0 sq.cm. Porting the MAF sensor housing by cutting away the bar and grinding the cut edges smooth with a Dremel increases the cross-sectional area to 36.5 sq.cm and improves airflow by 35%.
The stock air filter is also restrictive, flowing just 416cfm at 1.5"Hg depression when new and is an even bigger restriction to airflow when dirty. Clearly, there's plenty of room for improvement!
The C&L 76mm MAF sensor housing has a much bigger 41.0 sq.cm cross-sectional area and flows 52% more air than the stock sensor housing. The C&L MAF kit includes the sensor housing, a 76mm diameter powder-coated airtube, a monster sized K&N filter, and a plastic heatshield to isolate the filter from the engine compartment. Replacing the whole intake system with the C&L kit produces a dyno proven 10hp/8lbft gain at the rear wheels.
I bought the kit that's calibrated for the stock 19lb/hr injectors (part no. CL-118) and reused the factory MAF sensor. If I upgrade to 24lb/hr injectors later on when I do the H/C/I swap, all I'll need to do is change the sampling tube for another C&L unit thats calibrated for those injectors. The kit comes with comprehensive installation instructions, is very easy to install, and looks great under the hood.

Ford Racing Intake Plenum Spacer Kit

I chose the Ford Racing 1/2" thick phenolic spacer (part no. M9486A51) for the stock EFI manifold. A 1" thick spacer is also available but raising the upper intake manifold this much can cause clearance problems with the factory strut tower brace.
The Ford Racing kit came with all the necessary hardware and it was very easy to install but it wasn't all plain sailing. Firstly, the brittle plastic vacuum hose T-fitting at the back of the manifold broke so I replaced it with a brass T-fitting from a building supplies shop. Secondly, the two long bolts in the spacer kit were about 1" too long so I had to insert spacers under the bolt heads in order for them to torque down. That meant that I couldn't put the 5.0 HO plate back onto the manifold so I left it off.
Since I planned to install a 75mm throttle body, I enlarged the inlet opening of the upper manifold to 75mm while it was out of the vehicle so that it matched the bore diameter of the throttle body. The manifold opening narrows down gently along its bore, funnelling air into the plenum and increasing its velocity for good torque production.

Without the spacer, the intake manifold temp. stabilizes at ~70*F higher than the ambient temp. when the engine's hot and idling with the hood open. With the phenolic spacer in place, the intake manifold temp. stabilizes at only ~40*F higher than the ambient temp. under the same conditions, proving that the spacer really does reduce intake manifold temperature.

Summit Racing 75mm Throttle Body

The stock throttle body (bottom of photo) has a tiny 60mm bore (cross-sectional area is a pitiful 24.7 sq.cm) which restricts airflow at higher rpm. The low budget hotrodder can bore it out to 62mm but that only improves airflow by 7%.
The Summit Racing 75mm throttle body (part no. SUM-227215) has 61% more blade area (cross-sectional area is 39.7 sq.cm) and flows correspondingly more air. It's a high quality piece and it comes with a full set of installation instructions.
Installation was very easy except for a couple of "gotchas". Firstly, the bolt holes were too small (8mm) making it difficult to mount the throttle body onto the intake manifold elbow, but drilling them bigger (10mm) solved the problem. Secondly, the two Philips screws holding the TPS in place were very tight and needed a lot of persuasion to come out.
Though the HP/TQ gain is insignificant on a near stock 5.0 engine, throttle response is much improved and the larger throttle body is essential when more performance modifications are added later on.