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I think the factory exhaust on my 2000 7.3l Exc is 3.5" or at least that is what is on there now. How much of a difference will 4" make???? I do have the Edge Evo. programmer?
I think it's more important to 'unrestrict' the flow of the exhaust. A free flowing through muffler and a cat delete pipe would be the best bang for the buck, imo.
The aftermarket exhausts, like MBRP, are mandrel bent for less turbulence around the bends. Also the extra .5" in diameter gives an extra 1.5" of area inside the pipe to help flow things a bit better.
The stock exhaust is indeed 3.5 inches with alot of restriction, the biggest being the muffler. If you upgrade to 4 inches like I did, your turbo will spool up faster and respond better all around.
A diesel engine is basically a gigantic air pump, the more air in/out you give it, the better it performs.
4 years ago my truck was stock with just a K&N filter and averaged 17-18 mpg, but you really had to push it. I added an AFE stage I and it helped, but it still needed more. Spring 2006 I added a 4 inch MBRP system and an Aeroturbine muffer and it really opened things up. After the exhaust I averged 17-18 much easier with a quieter, better performing engine. Shortly after, I added my SCT programmer and with my truck in it's current configuration, I easily get no less than 18 mpg mixed and as high as 20 mpg when I'm on the open road.
So it is worthwhile, your truck will sound way cooler too!