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Thank you for using Just Answer. Is the cylinder 3 misfire the ony code you get? When do you notice the symptoms most - first start in AM?, When at operating temperature?, Cool days/hot days?, etc.
If you used any other kind of plugs besides NGK or DENSO, I recommend you replace them and only use these 2 brands. I don't believe that to be the source of your concern, however. You need to proceed to looking at your ignition coil. It is mounted in the distributor. Here is a link for you to see a breakdown of the coil.
What you will be looking for is any cracks, burn marks, pin holes, or white residue on the top of this coil. You do not have to completely remove the coil to inspect it. Remove the distributor cap and rotor. Remove the dust shield (it is clipped in place - be careful no to break the clips), then inspect the top of the coil. it is fairly common for those coils to go bad causing misfires and driveability issues.
I would recommend a thorough inspection before you purchase another part.
How long ago were the plug wires replaced, and with what brand? What brand of plug is installed. I recommended that you inspect the coil before replacement. I'm sorry you spent money that you didn't need to.
I also replaced the distributor cap and rotor. Sorry I didn't mention that before. I'm running out of options!!!!!
Lets step outside the box for a minute. I want you to check 2 things. They are not likely to cause this kind of concern, but I'd like to rule them out. Heres a link to the picture of the throttle body.
The IAC valve on the bottom could be a concern and could cause intermittent problems. You should try cleaning it with some Carburetor cleaner. Just remove the Air hose between the air filter housing and spray the cleaner into the throttle bore. Move the throttle plate by hand to clean around it, and make sure you get some of the cleaner into the air inlet at the bottom that goes to the IAC valve. Let it sit for a couple of minutes, then start engine. It will be hard to start, and will run really bad for a bit and will smoke a lot which will all get better after the cleaner has gotten out of the system. After that, see if it runs any differently. Next thing to check is the MAP sensor. It is mounted to the firewall and has a vacuum hose going to it coming straight from the intake manifold. Unplug the connector and check for around 5 volts DC at the outer 2 connectors. Turn ignition off, reconnect connector. Now it gets a little interesting. You will need to back probe the connector with it plugged in. This is easiest with some 'T" pins like the ones used for arts and crafts and can be found at Michaels or Walmart. You are going to want to see what the computer sees. You want to connect the negative lead to the brown wire, and the positive lead to the light green/redstripe. Turn the ignition switch on, but do not start the engine. You should read very little voltage. Start engine, and watch voltage, it should increase to approx. 1-2 volts.