The late model Mustang that rings a bell in any blue oval enthusiast’s mind is the 2003-2004 Mustang Cobra. At 390 factory-rated horsepower, the supercharged 4.6-liter 4-valve modular engine produced more power than any other late model Mustang in history at the time. Not only were they fast from the factory, but they also took very well to mods.

Case in point, our white 2003 Cobra that ran in the 10-second range on all stock internals. With an upgraded Whipple supercharger, 20+ psi of boost, cat-back exhaust, injectors, upgraded throttle body, and headers, our 4.6L 4-Valve was making 640 rear wheel horsepower. The risk of failure comes with any factory short-block that you push the envelope with, and that is exactly what happened with our Cobra.

During one ill-fated drag strip outing, we burned up a few pistons. Because of this, we yanked the engine out and sent it up the road for an overhaul to the well-known blue oval shop, Ford Performance Solutions.

You’re probably very familiar with our Snake. The aforementioned 2003 Cobra was produced for two years beginning in ’03, signifying its 10-year SVT heritage by producing an over-the-top 32-valve, supercharged mod motor that made nearly 400 horsepower. Although there were nearly 20,000 Cobras built during those two years, they have maintained a higher value than any other mass produced late-model Mustang due to its brutal horsepower achievements in both stock or modified form.

Ford Performance Solutions Knows Mod Motors

“We had been building modular motors since 1995 after the Lincolns came out,” said FPS owner Troy Bowen. “We bought five of the test motors from Ford, and began dissecting them. We then went to Ross to custom make some pistons before anyone else made them. We even did CNC work on almost all the heads they had, even the Titan V-10s. We started getting popular with the Cobra heads and working with the guys that were doing forced induction on them. That’s how we got our start”

While pumping out over 670 horsepower to the wheels and running mid 10-second passes, the long block was performing unbelievably in pure stock form. While its fair share of fun would be had from this, it eventually went kaput. Detonation mixed with worn piston rings turned this Cobra into a 2-stroke engine, burning as much oil as it did gas. In addition to the worn rings, 4 melted valves and multiple lost valve guides added insult to injury.

It was time to rebuild the 4.6L step by step, using upgraded pistons and rings from JE Pistons, boring the block with fresh FPS machine work, and adding some of the best valve train components from COMP Cams, and Ferrea. We’ll even top her off with an Aeromotive Fuel Rail kit, and we’ll be ready to lay down 650+ reliable horsepower that will actually live without eating itself.

The Build: Bottoms Up

Let’s start out by reviewing what components we are going to be using in the bottom end of our 4.6L:

  • JE Pistons 9.2:1 Compression for Supercharged Applications
  • JE Pro Seal Rings
  • Manley Rods (Stock) – Resized
  • Stock Crank (Forged Steel)
  • Pacific Performance Head Stud Kit #1564101
  • Pacific Performance Main Stud Kit #1565401

The first course of action to remedy the problem was to get the stock engine torn completely down. When Ford made the supercharged ‘OE Cobra 4-valve, they opted for an iron block in order to increase strength for the boosted application. “The 2 versus 4-valve blocks are very similar, though the 3-valve blocks are almost their own block and makes part interchanging difficult,” Troy says. The only cleanup needed on the block was a slight .020 over-bore done on the sleeves at FPS. Head bolts were trashed in favor of a Pacific Performance 8740 chrome moly studs and for the bottom end, the mains received a similar chrome moly stud kit. The stock crank (forged steel) and Manley rods were reused, and then it was time for the pistons.

We went to no one other than JE Pistons for some of their finest slugs designed for the 4.6L Modular engine. JE built us a set of custom pistons forged and CNC machined from 2618 Aluminum. These were designed for use with supercharged applications (as well as nitrous or turbo) and utilize 1.5mm, 1.5mm, 3mm rings. JE also include the pins, spirolox, and a full set of JE Pro Seal rings.



The JE 9.2:1 dish pistons are intended for a 3.552-inch bore. The tops of the pistons have been thermal coated to help prevent further detonation, and the skirts have a dry film lubricant to aid in any oil starvation problems in the cylinders.


FPS Engine Builder “Sam, the Super Man” sets the ring gap in the cylinders before installing the JE Pro Seal rings on the pistons

Hung to the JE pistons are the stock Manley H-beam rods. Ford went with these premium rods in order to ensure years of problem free service, and these were going to be more than adequate for our power needs. The crank is again a reused stock Forged Cobra crank that was cleaned and micro polished, and finishing up the short block was a set of OEM main bearings. Now, it was on to the long-block . . .


Long-Block Dreaming

Horsepower is almost always in the long-block. To that end, our major upgrades were a full set of COMP 4.6L 4-valve Modular camshafts, CNC-ported 4V heads, Ferrea stainless valves, and COMP valvetrain. All of those would help the 3.3-liter Whipple make big efficient power, with the Aeromotive Fuel Rails providing the fueling.

Here’s what we used:

  • Ferrea 37mm stainless intake valves #F1450P
  • Ferrea 30mm stainless exhaust valves #F1451P
  • Ford Performance Solutions, Complete CNC Portinp
  • Comp Cams Beehive Valve Springs – 324 lb/in Rate #26123
  • Comp Cams Titanium Retainers – 798-32
  • Comp Cams Modular Camshafts – 106360 – XE266BH-116
  • Aeromotive Fuel Rail Kit – 14122

Let’s start with the CNC-ported 4V cylinder heads from FPS:

Again, as with the block, the heads were torn down to bare castings, and the first action was to weld up and repair the melted combustion chambers. From there, it was time for some machining, starting with a valve job to accommodate the fresh Ferrea valves that were going to be installed. The final machine that the heads made their way to was the CNC. Both the intake and exhaust ports got a moderate porting job to help flow the larger amounts of air being crammed into and out of the cylinders.

The stock intake ports originally flowed at 238 CFM at .800 lift and now flow 293 CFM, a 50+ cfm increase. The exhaust ports increased even more with 165 CFM at .600 stock and then 253 CFM ported. “The 2-valves are very limited in the short turn areas of the head,” Bowen stated. “The low floor as it rolls into the port is flat, and goes right down into the valve seat. The 4-valve has so much more area, it is just like a pocket of valves. We have picked up over 100 more CFM in porting. We have got them up to 325 CFM on the intake port. The 4-valve 5.4-liter GT heads are even nicer, as they raised the floor to help out with the short turn.”


4-Valve Valvetrain: Double the Fun

When building a 4-valve over head cam engine, you get double the fun. Double the valves, double the cams.. and double the complexity. Luckily we had some good partners like Ferrea and Comp Cams.

Assembling the heads started with new bronze valve guides wrapped around Ferrea’s Competition Plus 4.6L Modular intake and exhaust valves. We settled on 37-mm on the intake and 30mm on the exhaust side, which are stock OEM replacements. These valves feature top of the line heat treating, and can even be used with the OE-style multi-groove style keepers. Other features include hard chrome stems, swirl-polished and under-cut stems, and cobalt-hard tips.

Controlling those Ferrea’s valve movement was a set of Comp Cam’s latest Modular Beehive “Ovate-design” valve springs, good for up to a .500-inch lift cam. Plus, they don’t require any machine work to fit.. yup they go right into the stock spring seats. They offer 90 lbs of seat load @1.47-inch of installed height, and 252 lbss of open load @ .970-inch installed height. The valve springs were held in place with Comp Cams Titanium retainers, lighter than the stock steel stainless retainers, and are also heat-treated to increase strength to the 6AL4V alloy.

Next up, something to snap open and then close those Ferrea valves: four of the very finest of Comp Cams “XE-R” 4-valve camshafts. The cams we selected are perfectly suited for a supercharged street car like our Cobra, while also having favorable attributes for the 1320. This cam is a stocking cam for COMP, and it’s optimized with a 116-LSA for forced induction like we mentioned, with a 1,500-6,000 rpm curve.

It was time to sandwich the heads and block together with our Cometic MLS head gaskets. Next, it was time to move to the timing chains since this was a DOHC engine. It’s important to make sure you TDC the engine and mark the chains so they are in the right place. Being off even just one tooth on your chain can result in a bent valve.

With the engine flipped on its head, Sam installed our new Canton Racing Products 7-quart oil pan. The pan allows us to keep the engine temperature lower while keeping the oil close to the pick up with the anti-slosh baffle. There is also a 1/2” NPT hole in the pan for adding an oil temperature gauge down the road.

For increased induction, we had to start with the additional fueling needed. The new 72 lb injectors were secured by Aeromotive’s new fuel rail kit that was designed specifically for the 4-valve power plant. Aeromotive includes all the lines and fittings you need, even a convenient adapter piece that will utilize the factory fuel pressure sensor.

To aid in the Cobra’s previous power, the blower was already upgraded to a 2.3-liter Whipple Charger that saw over 20 psi. But in an effort to cram even more boost into the motor, we upgraded the blower to Whipple’s 3.3-liter version that can produce up to 30 psi, which is approximately the same power as the 2.3-liter, but on less boost.



Final Thoughts

Now that our engine build was coming to close, we asked Troy what he thought the potential for this engine was, and what we should have learned. “First off, you did the right thing by putting good JE pistons and good rings in it,” Troy said. “Next, you addressed the head and intake flow with the ported CNC heads, and the Ferrea valves. Make sure good port work is done to the intake. Once the port is cleaned up and working right, it will help with the combustion problems. Finally, you picked some good mild cams. You don’t need to get aggressive and radical with a 2003 Cobra engine, the supercharger is providing plenty of boost to make the power with solid reliability.”

“Tuning is very critical on a modular motor,” Troy continued. “They are very quick to detonate and you need to make sure that the timing and fuel curves are on key. The way the fuel enters the chamber, it doesn’t have a lot of swirl. The fuel wants to throw fuel across the valve over to the far side of the exhaust.”

“What happens is you have a denser fuel charge by the exhaust, so it burns from the intake to the exhaust side, so they have a hot spot on the far side of the piston. Some shops will start with a centrifugal map in the ECU when tuning a roots style modular motor, and they end up killing the motor. Since the Whipple’s are positive displacement, they are already making boost at 2,000 rpm. You have to immediately pull the timing out of them…”

Eagerly Waiting the Installation

While we can’t complain that we got over 11,000 highly abused miles that included over 40 runs at the track with it, it was inevitable that the stock engine was going to slowly pass away. With a gaggle of low 10-second runs, we knew that was needed to build was reliable power, not really more power.

Ford Performance Solutions was very helpful when it came to building this fresh 4-valve that we hope will produce an additional 300 horsepower to the wheels over a stock 2003 Cobra. Troy and the team assembled the engine with all of our quality goodies, and soon we will be putting the 4.6-liter back into the Cobra for some tire roasting fun. We’ll bring you an update as soon as we stab the engine in!