First off, start with your engine choices. Lincoln Mark VIII engines are cheapest but the intake isn’t so great and you’ll have to deal with IMRC plates. The IMRC plates create better low end torque over the newer 4v heads after 1999. I’ve heard of people using these with a nitrous window switch but that’s up to you. I’ve noticed the prices of 4v engines rising lately. You can probably find a decent Mark VIII motor in any junk yard and snag it for about $700-$1000. They did come with the strongest aluminum blocks made in Teksid, Italy. These blocks go for about $400 alone and are great for any 4.6 build up. Don’t bother with the Continental 4v blocks because they’re front wheel drive and missing one of the motor mounts, oil filter on the opposite side, etc. Another Lincoln 4v 4.6 worth swapping in is out of the Lincoln Aviator SUV. Better heads and cams then the older Lincoln 4vs and older Cobras but the intake is taller and I’m not sure if it fits under a stock Mustang hood. The Aviator motor has the same heads and cams as the Mach’s, 03/04 Cobra’s, and Mercury Marauders. However, all the Lincoln motors came with the weaker 6-bolt cast iron cranks. Another thing to take into consideration for the swap is whether or not your car has a 6-bolt flywheel (96-98 and 01-04 GT) or an 8-bolt flywheel (99-2000 GT). The stock GT flywheel will bolt up to the corresponding number of bolt crank. Aviator motors have been going for around $2700. If you plan on swapping an older Cobra motor into your GT, you might want to take into consideration what type of fuel system you have. If you put an older Cobra motor in a 99-up GT, you’ll have to either convert the fuel system to return-style or get return-less fuel rails for the Cobra motor, not to mention changing the ignition to distributor-less or going with coils and spark plug wires. The older Cobra motors are a little cheaper than the 99-up 4v’s but its hard to find one with lower miles. All Cobra motors come with forged 8-bolt cranks and aluminum blocks with the exception of the 03/04 Cobra with iron blocks. In 1999, Ford improved the cylinder head design on the Cobra making more horsepower and torque. The heads are known as tumbleport or “C” heads. Pre 99 4v’s came with twin port or “B” heads. If you had a 98- older 4v but wanted the higher hp tumbleport heads, you can swap from a Continental 4v after 1999 or any 99-up Cobra/Mach/Marauder/Aviator heads but you’ll need a 99-up intake manifold to make it work. I used a 2001 Cobra intake manifold on my Mach longblock. It’s pretty much the exact same intake minus the shaker system brackets and the snake emblem and the lower is the same. I’ve seen these intakes go anywhere from $350 to $550 un-ported and $650 or more ported. Look for an intake with all the sensors, fuel rail, injectors, etc. These parts add up, trust me. Your tuner will probably recommend an EGR delete as the kit costs around $20 and looks much cleaner. Ford rated the 99 and 01 Cobra’s at 320 hp and under-rated the 03/04 Mach 1’s at 305 hp. Dyno’s have proven the Mach’s to measure as much as 10 rwhp higher than the 99-01 Cobras. Like I said earlier, all Cobra’s came with 8-bolt forged cranks. If your Mach motor is out of an automatic transmission car, it has the cast iron 6-bolt crank. Only manual transmission Mach’s came with the 8-bolt forged crank. However, all Mach’s came with aluminum blocks. There was a website about 2v-4v swaps that claimed Mach 1’s to have iron blocks but this was not true. Prices on the 99-01 Cobra and Mach 1 engines are around $3000 to $3500. If you have lots of money to spend and you want a forged shortblock that’s already supercharged then look for 03/04 Cobra engines and you’ll spend anywhere from $7000 and up for the motor alone. I’ve seen a lot selling with a T56 for $10,000 or more. Overall, getting a complete engine is key. The little things can add up quick and that takes money away from other things you’ll need for the swap. Things like gaskets, bolts, sensors, etc. For example, DOHC cam cover bolts from Ford will cost you almost $8 a piece and you need 20! I went to the junk yard and got them for $5 total from a Mark VIII motor. Your oil pressure sensor and coolant sensor will change over as will your power steering pump, A/C compressor, but I’m not too sure on all the A/C lines because the front covers differ between the years. There was no problem on my 99 GT and 03 Mach engine.
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http://www.modularfords.com/threads/91637-My-2v-to-4v-swap-write-up