That is a tough one.
Let me see if I can help you. I am going to try to use some past experiences.
Way back in 1997, I got a 1980 Mercury Zephyr with about 250,000 miles on it for a girl I was dating. The car cost me $100.00. I did a tune up and replaced the plugs, wires, cap, and rotor. I took it for a ride, everything seemed OK. I hear a loud ticking noise under the car. I looked underneith and the catilytic converter was bright orange. After some research, I figured out I had two plug wires mixed up. The converter was getting blasted with unburnt fuel and it was causing the converter to heat up. Switched the wires and started it back up. After a few minutes, the converter cooled off enough and it was no longer orange.
So, I am going out on a limb here, but I think you have eother a wire or two mixed up, or a plug or two is bad. Take it to Autozone and have them check the codes. You can also invest in a code reader and check the codes yourself.
Before you do anything, check the wires. The coil pack should be labled to which plug the wire is suposed to go to. I mis-fire is easy to diagnose with the OBD-II system. If you get any of these codes, it will tell you what is going on.
P0300-Random/Multiple Cylinder Misfire Detected
P0301-Cylinder 1 Misfire Detected
P0302-Cylinder 2 Misfire Detected
P0303-Cylinder 3 Misfire Detected
P0304-Cylinder 4 Misfire Detected
P0305-Cylinder 5 Misfire Detected
P0306-Cylinder 6 Misfire Detected
Check that clinder to make sure the plug is in good shape or if it needs replaced.
I don't what you had done to it when you had the original misfire, but I would start there.
Tom