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My truck has the stock exhaust with the muffler deleted. It also has stock air box. Will an aftermarket air filter/box and 4" exhaust effect the egt's, fuel economy or performance? And if so, which brands?
To answer your questions, it will lower egt's, help turbo spool up, and maybe help a bit on fuel mileage.
It will filter much much better than the stock junk as well.
The best hands down is the AFE Stage 2 intake system.
The ford ais works well too but doesn't flow as much.
A cheap alternative to both is the DIY/6637/Tymar intake. Which is a NAPA/Fleetguard PN 46637 filter, clamp, and piece of 4" hose.
Less than 50$ and does a dang good job of filtration and flow.
I picked up 1.5 sold mpg's when I did the intake and exhaust. Not saying you will see this gain, but that is my experience.
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