Air filter... I bet you changed that and didn't put it on the list, but it's worth saying.
Slack in the accelerator cable - Known issue where the cable stretches so WOT is actually only 2/3 throttle plate. Put something on the accelerator pedal and check the throttle plate. If it isn't open all the way, there is a thread on how to... I guess shim it, I'd say. Here is the link:
http://www.explorerforum.com/forums/showthread.php?t=242299
Compression Test - This is really the first bonified test I would do to gauge an engine. If it doesn't have good compression across the board, nothing else is going to make up for it.
Fuel pressure - Lowish fuel pressure produces poor injector pattern, incomplete burn, putt putt from exhaust. Buy a cheap gauge and check it out. Fuel pressure test link:
http://www.explorerforum.com/forums/showthread.php?t=142801
Spark - You have spark because it runs, but I have heard of people swapping in a new coil pack and getting results. Pull a plug and put it back on the wire, ground the plug and crank the engine to check for spark quality.
Vacuum - Go through your lines, check for loose connections and leaks.
Are there any check engine codes stored? Delete everything and start fresh. Maybe you will catch something here.
Mass Airflow Sensor - It never hurts to pull this and clean it. I do it during oil changes because it really is so easy to get to and verify.
Cat Converter - Any other exhaust reduction, i.e. crushed pipe. Actually, there is a vacuum gauge test, measure vacuum at idle and compare it to vacuum at a steady 1500rpm. If vacuum drops substancially, the cats are suspect. I have heard of people removing the o2 sensors temporarily, substancially better performance indicates bad cats or some other obstruction. If you do this, you will get some false engine codes to deal with. I once saw a guy use a crayon to draw lines on the pipes before and after the cat as well as lines on the cat itself. I think he was using the time to melt as an indicator of exhaust flow. Clever, but I have no idea how to really do it myself.
When you pulled your plugs, was there anything to describe? Old spark plugs are one of the best diagnostic tools.
