I work in the parts department of a Ford dealer. Just picked up an '03 about 4 weeks ago. I didn't want anything having to do with cam phasers or solenoids. That alone, sent me to the '03 and '04 model years. I also didn't want any auto suspension options. I looked at so many '97-02 Expeditions online, I got to where I could tell which suspension it had just by the way it sat, LOL. With the '03-04, just look underneath and look for coil springs on the front AND rear suspension. I too, preferred 2wd with heavy trailer tow. No sunroof. No DVD entertainment system. Just more stuff to go bad or have problems with. Most of the CD6 radios have issues with the CD player. I'm waiting to replace mine with an aftermarket head unit. Knocking, popping in the front end could be either ball joints or sway bar end links. I ended up replacing everything on mine. It has 167,000 miles on it.
Take it for a drive and listen to it. Excessive wind noise could be collapsed weatherstrips, tweaked door frames or latch issues. Groaning from the rear end limited slip clutches could be more trouble.
Ask if the spark plugs have been done. The '03-04 generally don't have breakage issues, but they could have that one plug that blows out.
Half the lock and window switches in mine didn't light up. Ok. More than half. Run the rear air controls to see if you hear any popping. The blend door motors are not durable. If you are looking at one with heated and cooled front seats, make sure they work. If you're checking it when cold, hit the heated half and the switch should light up red. To check the cooled half, I believe you have to have the A/C on. Hit that half of the switch and it should light up blue. Mine weren't working when I bought it. Luckily, reprogramming both climate controlled seat modules brought them both back to life.
Look at the A/C compressor and see if there is any green oil hanging off of it. If you end up needing a new compressor, well, they aren't cheap from Ford.
Inspect the rear tail gate for corrosion or paint bubbling, especially around the handle area. They are aluminium and Ford had issues getting the paint to stay on. Hopefully they have figured it out with the new F150. Weatherstrip around the liftgate glass opening can shrink. New ones fit better, but not perfect. Open the liftgate glass and push the weatherstrip out in the corners to check it.
There is a place or two in Texas that reproduces the front seat covers. The Seat Shop is one.
If you're buying one to use the 3rd row seat for passengers, you might look at the 40% (RH) seat. On that seat, the LH side hinge cover and seat belt receptacle can have issues from the shoulder belt on the middle seat getting hung up during up/down movement.
Look at the heater hoses and control valve on the passenger side of the engine for any signs of coolant leakage.
Check that the power pedals move more than an inch. I hadn't checked mine until I found a post (reading every page of ALL the forums while at work has merit) regarding an issue with the gear inside the mechanism. Like the blend door motors, the plastic gear breaks. Curless Automotive sells a brass gear ($85) to fix it. My gear showed up today. Should take 20-30 minutes to replace it.
If the turn signal on the bottom of the mirror looks like it has junk in it, it is most likely the chrome coming off the reflector inside leaving the black base plastic underneath showing. It's all glued/molded together, so replacement is the only option.
Step up on the running boards and inspect the roof panel seams in the channels next to the roof rack for rust.
Mirror motors. I had to replace one. Not too hard. The option for the mirrors to dip/tilt when in reverse can be turned off, and that helps save the wear and tear on the motors.
I prefer no tire pressure monitoring system, but others may prefer the safety of such government intervention and additional maintenance costs.