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First check the plugs. Pull the #6 plug and look at the electrode. If it's wet and/or dark (black) it's probably not firing correctly. What is the spark plug gap? Is the center electrode eroded (not flat on the end)? Swap in another plug and see if it makes any difference. How old are the plugs?
Second, check the wires. Did you replace the wire(s) when you changed the coil pack? They should be replaced periodically (I replace the wires on my '96 4Runner at about 100k miles). Check the wires with an ohmeter. Resistance should be around 16-17.5k ohms (depends on length).
FYI, each coil pack on your vehicle fires two spark plugs. The #6 spark plug is fired by the #3 cylinder coil pack, so if the coil pack were bad, most likely both the #3 and the #6 plugs would not fire.
Check spark at spark plug using a spark tester and fuel pressure at the rail when it acts up. If the pressure is ok at the rail, but the injectors aren't firing, that can point to a bad computer.If the fuel pressure is present but the spark is not being supplied to spark plug wires to spark plugs, then an ignition module might be in need of replacement (the metal plate the coil packs sit on). If the engine has a service engine soon light before it dies, maybe check the codes that should be stored in the computer using an OBD-I scanner.
The coil packs are numbered 1-4,5-2,3-6.The firing order is 1-6-5-4-3-2.The 1-3-5.cylinders are in front and the 2-4-6 are in the back.There are 2 types of coils.Type 1 the coils are all in one pack.A complete system.Type 2 the coils can be replaced separately.(ie.)1-4 are separate and 2-5 so on.Good luck.
Here is a diagram of the firing order for you 3800 engine. Cylinders 1 and 4 are misfiring because the operate under the same "Coil Pack" and the coil pack has unfortunately gone bad. O'Reilly sells them for between $30-50 depending on the amount of warranty coverage you want. To replace, simply unscrew the screws that hold the coil pack in place. WAIT before unplugging the plug wires. Place the old coil pack and new coil pack next to each other, unplug one plug wire, then plug it to that same port on the new coil pack. then do the same for the other plug wire. Then screw your new coil pack in place, and start you car. should run fine!
I would check to make sure your spark plug wires are not coming loose from the coil packs on the back of the engine, i had the same problem with a '97 cavalier and then the check engine light started to flash meaning it had a catalyst threatening mis-fire.
also check to make sure you have the correct order, these things will run with the wires mixed up but they are gutless.
a new fuel filter might not hurt either, they are easy to change located near the back axle, one nut and a quick connect fitting.
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