Displacement Test-4.6L VS....
Displacement Test-4.6L VS. 5.0L
This Test illustrates the gains offered by increasing the displacement from 4.6 liters to 5.0 liters. In truth, the 5.0L combination benefited from a slightly higher static-compression ratio as well as cam timing that offered 4 degrees of duration, but the difference in power is interesting between the two displacements. Note that the 5.0L combination improved the power output throughout the rev range. The power gains cannot be attributed to the compression or cam timing, as bigger motors simply make more power and torque.
Another area that can be exploited to enhance the power output of any Two-Valve combination is compression ratio. This is one of the reasons for the popularity and effectiveness of swapping PI heads onto an early non-PI short-block. The difference in the combustion chamber size between the two heads (51 cc vs. 42 cc) means the swap will offer a significant jump in static compression ratio (over one full point). So, in addition to the flow improvements offered by the PI heads, installing them on the early short-block also improves performance by upping the static compression ratio by roughly 1.3 points. Conventional wisdom (and dedicated testing) suggests that every point in static compression will increase the power output (throughout the rev range) by roughly 4 percent, thus the extra compression can be worth as much as 20 hp on a 400hp Two-Valve combination.
Testing for my book Modular Performance (Building 4.6L/5.4L Ford Horsepower on the Dyno) demonstrated that installing a set of ported PI heads (ours came from Total Engine Airflow) and a matching PI intake on an early non-PI short-block was worth over 90 hp. Imagine that; swap out the stock non-PI top end for a set of properly ported PI cylinder heads and the matching intake manifold, and you've got yourself an extra 90 hp. That's like adding a blower or nitrous, but with fewer hassles.
There are, of course, additional avenues for power, including the exhaust system. As with the induction system, exhaust systems are often misunderstood as well. Everyone's mindset seems to be focused on increasing exhaust flow, but like the intake manifold, (long-tube) headers were designed not solely with flow in mind, but with pulse tuning as well.

Adding A 3.75 stroker crank...

Adding A 3.75 stroker crank to your 4.6L block will increase the displacement to a full 5.0 liters. Now top that stroker combination with ported heads, a set of cams, and the PI intake, and you have one torquey (and powerful) street machine.

Things Such as synthetic oil,...

Things Such as synthetic oil, underdrive pulleys, and this electric water pump from Meziere all improve the power output of your mod motor.

Using Nothing more than a...

Using Nothing more than a top-end package (heads, cam, and intake), it's possible to increase the power output of your otherwise-stock non-PI motor by over 140 hp. Dedicated 5.0L stroker buildups have touched 500 flywheel horsepower, so don't be too quick to count out that Two-Valve.
Headers operate on the same principles as the intake manifold, only in reverse. The reflected resonance waves present in the exhaust system provide negative pressure waves to help scavenge the exhaust from the cylinders, which in turn helps draw in more intake charge. This scavenging effect is determined by the length and diameter of the primary tubing being used, as well as merge points for Tri-Y designs. Just like the intake manifold, headers are optimized for particular engine speeds and displacement, but since the start of the reflected wave is determined by the exhaust opening, the effectiveness of any header design is dependent on the cam timing as well. What this means is that there's no one design that is universally correct for all applications. Change just one variable in your engine combination, and you might well have changed the "ideal" header requirements. Aft of the headers, the exhaust system is merely a subjective combination of flow and noise quality, though x pipe systems can further enhance the power and aural gratification of any Two-Valve combination.
In addition to the stars of our "Bigger is Better" gala, there's also the supporting cast. Things such as underdrive pulleys, electric water pumps, and synthetic oil can all improve the power output. Unlike performance intake manifolds and camshafts, underdrive pulleys don't actually produce power so much as they reduce parasitic drag and power losses associated with driving the accessories. Also, be sure to gear your car correctly so the engine spends the bulk of its time in the proper rpm range for the type of driving you do, and of course, be sure to have a custom tune when looking for maximum power. All the parts in the world won't be worth a darn if the air/fuel ratio or ignition timing maps are off.
A good performance 4.6L Two-Valve buildup deserves nothing less.

Cam Test: Stock Non-Pi Vs....

Cam Test: Stock Non-Pi Vs. Comp XE274h
The 4.6L Two-Valve motors all respond well to changes in cam timing. In this test on an early non-PI motor, swapping out the stock cams for a set of XE274H Xtreme Energy grinds from Comp Cams showed significant power gains. The new cams offered as much as 40 extra horsepower, but note that there was a slight loss below 3,500 rpm. Some of the loss in low-speed power could have been tuned out by advancing the cam timing, but expect a trade-off in power with aggressive cam timing.

Cylinder Head Test: Stock...

Cylinder Head Test: Stock Non-Pi Vs. Total Engine Airflow-Ported Pi
Swapping Out the stock non-PI components for the later Power Improved version is always worth additional power. When you combine the benefits of the PI components with additional head porting, you have some serious power gains, as witnessed by this head swap from Total Engine Airflow. The stock PI motor was run first with the stock heads and intake, and then with a set of TEA-ported PI heads and PI intake. Everything else remained the same, including the short-block, cams, and exhaust system. Adding the ported PI heads and intake increased the power output by nearly 100 hp.

Header Test-Stock Pi Manifolds...

Header Test-Stock Pi Manifolds Vs. Hooker Headers
While Most enthusiasts think the power comes from the additional exhaust flow offered by long-tube headers, the reality is that the tubing length helps scavenge exhaust from the combustion chambers. The low-pressure zone created helps draw the intake charge, thus improving the power output. If exhaust flow were the only difference, we would not see power gains of this magnitude, nor would we see any gains down low in the rev range. Replacing the stock exhaust manifolds with a set of Hooker headers on this non-PI motor resulted in some serous power gains, from 2,500 rpm all the way to 5,500 rpm. The headers were worth over 30 hp at the top of the rev range.