Hey Chris,
Visual inspection of wires can miss breaks in the insulation. Here's what I would do:
When the misfire is present, pull and replace wires in sequence, noting if the misfire gets worse or not. Either you will find a wire that makes no difference plugged or unplugged, or the misfire will be random. In the first case, swap two wires completely, and see if the misfire follows the suspect wire or stays at one cylinder. If it stays at one cylinder, double-check the distributor cap, spark plugs, and fuel injector for that cylinder. If it follows the wire, problem solved
If the misfire is not present in one particular cylinder, then look for general issues in the fuel or ignition systems. The best way I have found to troubleshoot an ignition coil is to replace it with a known (often expensive) good one.
Best of luck! Keep us apprised of how it goes.
