Most common mods are the high idle mod. This would allow you to idle your truck up to 1200 RPM when warming the truck up. It is also used to prevent wet stcking during extended idle times. If you have an 05-up truck, it is an exceptionally easy mod to do.
For these years, tucked up by the pedal for the emergency brake, you will find a bunch of cut wires. Find the purple with the green stripe wire in this bundle. Apply 12 volts to this wire any way you choose, be it a switch or just a straight (fused) "key-on" 12 volts.
Once this is done, any time you wish to have a high idle, set the e-brake, have the trans in park and don't touch the regular brake. In just a few seconds, the truck will jump up to 1200rpm. To disengage the high idle, release the e-brake or hit the regular brake.
The "zoodad" is another common/easy mod to do. Basically all that you do for this mod is cut the fiberglass panel that is behind the grill to open a hole in front of the air filter inlet.
The updated fuel pressure regulator kit (cheapest one) is part number 6E7Z-9C165-B. It will run you about $38 through Tousley Ford (800) 328-9552.
If you ever have your turbo out for any reason, updating the turbo oil drain tube is recommended. It is also recommended that you replace the turbo oil supply line. These parts are to ensure that the oil supply to and from your turbo is not compromised. Both of the older parts have areas in them that could develop restrictions to oil flow.
Should you have an early 03 engine (built previous to 3/18/03..serial number 52777 and down) you can not replace the oil supply line without the separate purchase of the updated oil cooler cover. Whether or not it is worth all of that expense it up to the individual owner.
All three parts on the following link would be needed to remove/replace the turbo and update the parts:
0 Parts - Tousley Ford Parts Depot
Another common mod is the CCV reroute. This mod will remove the oily mist from your air intake stream. The crankcase vent is installed just previous to the turbo by the factory. This allows the oily fumes to be sucked through the air intake and eventually be burned off by the engine. The problem is that the oil in the mist drops out of the fumes as it cools. The oil then coats everything in the intake and can collect in your intercooler. There are many ways to accomplish this mod, but the most popular way is the purchase of a kit that has everything you need and is made by a member of this forum and sold through Stealth Automotive. Just be sure you choose the one for your engine. CCV Mod
Going this route will add a catch can for the oil and then directs the stench back into the intake (oil free) to be burned by the engine. Those that have vented the CCV report that the stench can be overpowering at times.
Of course, the EGR cooler delete is also very common. Plenty of this info all over the forum.