I just got done putting my engine back together after replacing the heads, gaskets, and water pump and it ran the same way. 1st things fitst. DOUBLE CHECK ALL THE PLUG WIRES. Do this 4, or 5 times. Have someone else check them. Its fairly easy to do and can save you an assload of time. im not 100% certian but im fairly sure the coilpack goes
Rear of car
1 2 3
5 6 4
front of car
Ive seen people mess up the front because its not in order. Most likely theres a sticker on the top of your coil pack that can guide you. If not. let me know and i can double check my book.
2nd. Get it running and stick a penny between the idle stop and the throttle. This will have it do a high idle and hopetlly keep it lumping. Get out a can of something combustable. Ive used brake clean with good success. And start listening for a whistleing or hissing. Spray it if you think you hear a whistleing. If you come accross a spot that has a vac leak itll cause the engine to jump up and rev. Sometimes this is hard to do though cause the computer will think the car is dieing and attempt to surge the engine on its own. If it surges..try it again. Good places for vac leaks are the egr connection (passenger side rear valve cover), theres also a little hose that connects to that pipe that i think runs the vents inside the car. Check around the super charger collar nut. Thats where mine was leaking like crazy.
I guess if still no dice, you can take out all the plugs and check them for knicks, scratches, gouges, over/under sized gaps. Also check the mass air flow sensor for garbage. I had an explorer that got a fuzzie in there somehow once. Be careful and blast some compressed air through it backwards (lightly). although the car should still idle with that problem.
Just trying to help out.
-dan