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SCT is the most popular programmer. Get it directly from a tuning vendor and they'll include one or two of their email tunes in purchase. 5 Star Tuning, Unleashed Tuning and More Power Tuning (aka, MPT) are the most popular tuning companies for the EcoBoost.
Exhaust is an entirely different question and is nearly all about personal preference. I personally hate the sound of the EB with aftermarket exhaust, but that's just me. Borla and Solo performance seem to be the better quality kits out there, with varying noise levels.
The exhaust system has a forward portion with the down pipes, and a rearward portion with the muffler. The power gains are found by upgrading the downpipes. "Solo" brand and "Full Race" brand fit well, with Solo being the more affordable.
The SCT device is most widely used by tuning shops so having an SCT X4 or Livewire gives you the most flexibility to buy custom tunes from most shops. SCT also has data logging capability so you can share data with your shop to refine the tune.
Leading Edge Tuning (LET) is an often overlooked company that is putting out great tunes that are conservatively safe, and backed up with EXCELLENT customer service, not to mention free updates for life. I did my truck upgrades in stages and I think I am on the 4th revision of my tune with LET and it didn't cost me a dime.
Rezvani's Latest Post-Apocalytic Monster Is a Ford F-150 Raptor Underneath
Slideshow: Called the Fortress, the 850-horsepower pickup combines Raptor underpinnings with military-inspired features, survival equipment, and a starting price of $285,000.