I'd first suggest making sure the plug wires are all snapped on tightly at both the plugs and the coil towers. Make sure the electrical connector is on tight to the coil pack assembly as well. I've seen that come loose and cause a pretty significant misfire as well.
Do you still have a check engine light? If so, what does the code indicate? If it's showing a misfire for a particular cylinder, pull the spark plug from that cylinder and see if it appears wet from fuel or abnormal in color.
If you are confident that the wires are good, plugs are good, and the electrical connection to the coil pack is good, then try putting an inline spark tester inline with each wire (one at a time) and look for a cylinder that isn't firing. If all 6 cylinders appear to be firing with the A/C on, but the miss is still present, then verify that all vacuum hoses and air intake tubing is properly installed and not cracked or split.
If still nothing shows up, then you may want to consider swapping around fuel injectors if you have a misfire code for a particular cylinder to see if the misfire follows the injector.
-Rod