If you have a stock throttle body that flows 600 cfm and a 75mm throttle body that flows 750 cfm, shouldn't the motor make more power with the larger throttle body? The answer is-it depends. If the stock throttle body doesn't represent an airflow restriction at the given power level, then it's likely the motor won't make any more power with the larger throttle body. The motor simply can't take advantage of the additional airflow offered by the larger throttle body. In contrast, a larger throttle body may feel like it has improved throttle response, but this is a simple function of the airflow versus throttle angle. If you open the throttle just 25 percent, the larger throttle body will offer more flow than the stock throttle body, so the motor will make more power at any given throttle angle-except wide-open throttle. This perceived power gain is what sells a great many larger throttle bodies to otherwise stock motors. On modified motors, larger throttle bodies have been shown to improve power-just don't expect huge gains on your stock motor.
The throttle body provides airflow to one of the most misunderstood elements in the internal combustion engine, the intake manifold. Many enthusiasts mistakenly lump the intake manifold in the same airflow-device category as the throttle body, that is to say that more airflow is better. In truth, the intake manifold is not a simple airflow device but rather a sophisticated resonance tuning system that all but determines the effective operating rpm range of the motor. Runner cross section and length dictate where the engine will make power.

Throttle Bodies and inlets,...

Throttle Bodies and inlets, such as these systems from Accufab, are popular upgrades for Two-Valve motors. While you shouldn't expect huge gains with a stock motor, they can be worth 10-15 hp on modified motors.

Obviously The stock PI intake...

Obviously The stock PI intake is a ton better than its non-PI counterpart, especially when topped off with an aftermarket elbow and throttle body. The long runners promote plenty of midrange torque production, while allowing the motor to run effectively up to 6,000 rpm.

Short-Runner intakes (Reichard...

Short-Runner intakes (Reichard Racing shown) offer power gains over the factory PI intake, but the runner length shifts the power production much higher in the rev range. We've tested the unit from Professional Products (not shown) with good results on a stock engine.
More than any other single component, the intake manifold determines not only the peak power potential, but the overall shape of the power curve as well. At the risk of oversimplification, intake manifolds are designed to produce efficient power at a given rpm range, with longer runners promoting power lower in the rev range than shorter ones (of the same cross section). What this means is just because one intake outflows another, it doesn't mean it's "tuned" to produce efficient power in the desired rpm range, nor does it mean it will even produce more power on your combination.
This is why most ultra-short runner intakes don't fair well in back-to-back comparisons with the stock PI manifold. The short runners were designed to optimize power high in the rev range, and the stock manifold has long runners for good low- and midrange power. While we may see elevated peak power numbers well beyond 6,000 rpm, the loss in low-speed and midrange power is usually not worth the trade-off, especially for a street motor. Remember, with the 4.6 we only need to fill 281 ci-not 302, 347, or even 408-so you don't need a huge manifold. In the case of the 4.6, the runners are especially long, and for the most part, they need to stay that way in a naturally aspirated 4.6-5.0 build, especially if the car is street driven.
Next in line are the cylinder heads. It's certainly true that the later Power Improved (PI) heads are better than their non-PI counterparts, but it's the head flow (or lack thereof) that really differentiates the Four-Valve motors from their Two-Valve brethren. Cylinder-head flow is a critical element in ultimate power production. Obviously, port volume and the attending air speed (velocity) come into play, but the airflow capacity of the Two-Valve head is the limiting factor in terms of ultimate performance.

It Certainly looks the part,...

It Certainly looks the part, but you have to have a serious high-rpm motor to take advantage of the Reichard Racing intake.

Other Aftermarket intakes...

Other Aftermarket intakes are available for the Two-Valve motor, including those from TFS, BBK (soon to be released), Professional Products, and even the Bullitt from Ford Racing Performance Parts (shown).

Adding A set of PI heads to...

Adding A set of PI heads to your non-PI motor is a surefire way to improve performance. The PI heads offer both improved flow and a jump in compression thanks to a smaller combustion chamber.