The best resource for PI 4.6L...
The best resource for PI 4.6L engines is the '01-and-later Mercury Grand Marquis and Crown Victoria. This car was likely a victim of L.A. road rage, but the engine was in good shape and intact.
The Cobra wasn't the only vehicle that featured a 4.6L four-valve engine. The '03 to '04 Mach One, Mercury Marauder, Lincoln Aviator, and the '93 to '98 Lincoln Mark VIII also have a version of this engine.
The 5.4 Four-Valve
The iron-block 5.4L (330-inch) engine is found in some Ford SUVs, and a similar engine can also be found wedged into cars such as the '07 to '09 GT500 and '00 Mustang Cobra R. There is also an aluminum dry-sump version in the supercharged Ford GT. The 5.4L from the '99 to '04 Navigator has an iron block and four-valve heads rated at 300 hp. It is likely the engine you will run into in the yard. The alternative is a crate engine from Ford Racing. Currently, you can purchase a supercharged 5.4L GT500 Cobra engine that makes 500 hp or the Shelby Super Snake 5.4L with the Eaton Twin-Vortices four-lobe 160-degree twist supercharger for 605 hp and 550 lb-ft.
In 1999, the SVT Lightning truck was equipped with a supercharged two-valve version of the 5.4 called the Triton V-8. Our sources agreed that these rare supercharged engines, as well as other naturally aspirated 5.4L two and three-valve engines can be tempting but have intake manifolds that choke down the horsepower and have limited aftermarket solutions. These engines are also packaged for trucks, meaning they are tall, wide, and less suitable for swapping into your Mustang.
This is the '99-and-later...
This is the '99-and-later PI intake port from the 4.6L cylinder head. Note the rectangle and dogleg. These engines can make an easy 450 hp with a Vortech centrifugal and the stock short-block.
Swap It!
So what should you swap into your early Mustang, Falcon, or Cougar? The dominant swap is the '96 to '01 iron four-valve 4.6L Cobra engine with a manual transmission. Instead of trying to find a Cobra in the yard, swappers were buying the complete drivetrains directly from Ford. Recently, Ford's supply of replacement Cobra engines has been drying up, forcing people to look for other sources. Ford Racing's answer to dwindling supply is the Aluminator, an aluminum version of the same engine with a forged rotator and '03 to '04 Cobra heads and camshafts. It is available with 10.0:1 compression or 8.5:1 as a true supercharger-ready Cobra replacement. The other source for the four-valve 4.6L is the '03 to '04 Lincoln Aviator, Mercury Marauder, or the '93 to '98 Lincoln Mark VIII.
To get the 4.6L four-valve into a '64 to '66 Mustang chassis, everyone agrees that the shock towers need some fabrication. Dimensionally, it is possible to install a four-valve engine without cutting, but this swap is about more than just wedging a modern engine into an old chassis. It's about jumping into a car that feels new with throttle response and handling and looks like an early Mustang. Initially, the barrier to entry was the expense of the modifications and the cost of the engine itself. Now complete engine kits are available that can be installed by do-it-yourselfers with a garage MIG and some car-guy skills. There is also a small window of engine availability because wrecked 4.6L-powered vehicles are starting to show up in the junkyard.
Another engine that is virtually free in the junkyard is the 4.6L two-valve. This is proving to be the budget-oriented swap for guys who want the wow factor of the big, modern engine in their Mustangs and Cougars and don't care to make more than 400 to 500 hp. To sweeten the deal, you can buy an Edelbrock carbureted manifold and chuck the fuel injection (or don't buy it), eliminating the hassle and expense of computer tuning and complicated high-pressure fuel systems.
We've included the details of a swap performed by The Mustang Shop in Auburn, Washington, some pointers from Year One about its swaps, and as much information about the 4.6L as we could, along with a quick junkyard tour that reveals what is available in the yards. It's not all the information to get a complete drivetrain into your car, but it might just be enough to get you interested in doing this swap yourself.