Make sure the engine is mechanically sound. It looks like you are already doing that and have replaced the Charge Air Cooler, which will help improve fuel economy. Then:
1. Slow down. This is the only fuel mileage upgrade that is ABSOLUTELY FREE and totally controlled by the driver. By letting your foot up on the accelerator, you will improve your fuel mileage and prolong the life of your engine. In particular, find your engine's sweet spot (which is usually between 58 and 63 MPH) and stay there as much as possible. Some trucks have it below 55 MPH (hence the 54 MPH club that Kevin frequently mentions), most have it just slightly above.
2. Replace the stock muffler with a performance muffler. Stock mufflers are made by Donaldson (the same guys that make the paper air filters), corrode easily, lose performance gains over time, and plug up with soot. I would suggest a Pittsburgh Power muffler instead. The $150 price tag is nothing compared to the improved performance, noise control and fuel economy.
3. Get air tabs. These will make the truck more aerodynamic by redirecting air flow. While you're at it, check all your extenders, skirts and fairings for damage and fix those when you get the air tabs on order.
4. Replace the mis-matched, recapped tires. Get yourself a set of Michelin XDA Energy tires, or if you're going to wide singles, get the Michelin X ONE XDA Energy. You'll gain fuel economy, improve your traction and make your truck safer.
5. Replace the stock Donaldson paper air filter with a Fleet Air Filter or a K&N HD Air Filter. The Fleet Air and K&N products improve air flow, are easier to service, and are lifetime air filters... They'll go hundreds of thousands of miles before needing replacement, your engine will breathe better and you'll get better fuel economy.
6. Turbo 3000D and/or FASS System.
7. OPS and Synthetic oil (Amsoil, Mobil One (also known as Mobil 1), Shell Rotella T5 or equivalent) IF the engine has no oil leaks.
There are some 60+ ways to improve fuel economy in addition to what I just mentioned. Let cheaper stuff (slowing down) pay for bigger stuff (tires).