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I'd for sure lose the mudflaps. I'd personally remove the running boards too, but some people like them and use them too. I think removing them makes the truck a bit sleeker and look lower. Wheels and tires are always the first thing you should upgrade IMO, as far as looks. A set of 20-22" chrome or polished wheels would look great, with a good fat tire. Something like a 305/55/20...etc...The truck has lots of potential for sure.
From the other side of the camp...you should get a nice 17 or 18" wheel with some 35" AT's or even a more aggressive tire. Removing the steps, in this instance, will make the truck look taller. I agree on the mudflaps, ditch those. Putting the 20" tire combo will nullify that it is a 4x4 truck.
My old truck was a 06 F150 SuperCrew Lariat 5.4 with the 6.5' bed. Lost a cylinder in early November. It could barely tow my 8500 lb TT in the Sierra's (foot flat to the floor on almost any grade). I traded it in on a 2008 F350 short bed, 6.4 PSD, FX4 with the Tuscany Upfitters package, 34,000 miles, paid $37,000 for the new truck. I love it.