Here's what I would do;
1. First check for a leaking FPR. If its good proceed to # 2
2. Find out what cylenders are not firing. There are two ways to do this. One way is to unplug each spark plug wire one by one (engine running), plugging them back in as you go, to find the one(s) that has the least change in how the engine is running.
The other way is to disable each fuel injector one by one through diagnostics mode with the engine running. To do it that way you enter diagnostics mode, and when it says "PCM?" you press the fan up button. Then press the fan down button untill you reach "PCM OVERRIDE?", press the fan up button to enter that menu. Then press the fan down button again until you reach "PS04". Leave that on the big LCD screen and press the cooler button (blue) and hold it down to disable the cylender#1 injector, then press the warmer button (red) to select the next injector and press the cooler button to disable that one (you should see what # injector you're on in the climate control LCD). Repeat this until you've gone through all 8 injectors and have noted which ones give the least effect on how the engine is running. Once you know what cylenders are missing move on to #3
3. Pull out the spark plugs in the cylenders that are missing. If they are wet with gas, you know the problem is most likely electrical (move on to #4) . If they are completely dry, and don't even smell like gas, its most likely a fuel related problem (move on to #5).
4. Follow the wires and see if the cylenders that are missing are being run off the same coil pack. If so, the coil pack is no good. If not, you have some bad spark plug wire connections (not snapped on all the way). Anything before the coil, the PCM would sense and throw a code. It could also be a bad EGR valve.
5. Change your fuel filter and see if that does the trick.
My god, I could go on all night, but I think I said enough to get you started. lol.
Hope this helps.