Maybe the most commonly asked question here on AFM. Seems like it gets asked at least once a week. A search should bring up numerous threads. Here's a general recap:
CAI + tune: either a JLT or C&L cold air intake (to increase the size of the MAF sensor) and an SCT xCal3 programmer (to reprogram your car's onboard computer to adjust the air/fuel ratio and spark advance to the larger intake air volume from the CAI, which is necessary to prevent running lean and possibly causing detonation). Stay away from any CAI that doesn't require a re-tune, as it is the tune/program that really adds the most horsepower. The programmer can also be used to improve shift quality if your car has an automatic transmission, and to correct speedometer readings if you add gears or change rear tire diameters in the future. Most people here on AFM like the SCT xCal3 better than the Diablo. The only reason to use anything other than the SCT would be if you want to have all your work done at a specific shop and they use and prefer a different programmer. Good shops like Bama and Tillman usually sell a package that includes the CAI, programmer and three canned tunes.
For installation, the SCT tuner gets temporarily plugged into the OBD port in your Mustang to download the chosen computer program (or tune) while saving and storing your factory settings in the SCT in case you ever want to remove the CAI and reinstall the factory airbox and factory tune. If you purchase additional programs (most shops sell three tunes with the unit) you can switch between tunes for different octanes (highest octane available in your area for best performance versus lower octanes for saving money on gas).
I recommend JLT intake with SCT X-calibrator 2 tuned by Evolution.
Before I went to a blower, I did the above, with the only other changes being flowmaster mufflers and 3.73 gears. They had me running consistent 13.50's at about 103-104 mph in an automatic. Since bone-stock, auto tranny stangs run about 14.1 - 14.2 out of showroom, I would say that's a pretty good result.
Go with the C&L Racer or JLT Series II intake and tuner package! You'll pick up a ton of horsepower, extract driveability out of the car, amazing throttle response! There's a night and day difference between a bolt-on K&N cold air induction system with no tune, and a larger MAF system like the JLT or C&L Racer system with a custom tune via SCT X3 Powerflash handheld programmer for us.
I have dyno results from a car that had a 93 octane "no-tune" K&N cold air intake system running extremely lean at WOT, and then from JLT/C&L Racer and tune combinations and you'd be surprised at the separation in RWHP/RWTQ even down low!
I have the C&L Street Intake and XCAL3. I got my main tunes (87,91,93) from Brenspeed. And I also purchased the 93 Race Tune from Bamachips, along with emission's tune. I use my 93 Brenspeed Tune everyday as the car seems to perform consistently and more stable with it, while at the same time slewing a few opponents on the highway. I use the Bamachip's tune every now and then when I leave the house with the intent to race. The Bama Race Tune is just a little more aggressive than the Brenspeed tune. With either tune you can not go wrong but as your daily driver the Bamachips Race Tune may be a little to aggressive. With My Bama Tune, my tires chirp (Only when I go WOT from a dead stop) from 0-1, 1-2, 2-3 gears. Brenspeed's 93 octane tune shift hard but don't give the same chirping affect, at least not in my experience. I have not tried Bama's other tunes so I can't speak on those. If these are your first Tunes, I would say go to Brenspeed first.
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