You didn't tell us what engine or how many miles on it.
To prevent damage from unburned fuel being dumped into exhaust, the PCM will shut off fuel to cylinders that it detects misfires for, that can cause a "miss" from a minor problem in the ignition to feel like a huge problem as you run only a couple of cylinders for a few seconds.
Faulty spark plugs or wires------Changed all plugs, good gaps
Faulty coil (pack)-----Replaced all coils
Do you have any other codes? i.e. a lot of the possible causes you mentioned would trip other codes as well, so a combination of codes can help you narrow this down.
You've replaced the spark plugs, what about the ignition cables/wires?
Does you engine even have ignition cables/wires, some Commander Engines do, some don't. The 3.7L V6 has all coils on top plugs in the earlier years and switched to only one bank having coils and the ignition cables/wires running to the other bank in later years. They do degrade and go bad. At the very least you should check their resistance and make sure they are under the acceptable ohms/foot spec for you engine/vehicle. How about the boots on the coils? Did the new coils come with new boots or did you reuse the old boots on the new coils?
When you replaced the plugs and coils, did you thoroughly inspect and clean all the old ignition parts? To include cleaning the electrical connectors on both sides (Coil and Wire Harness) with electrical cleaner and then seal the connectors with dielectric grease?
I had the same with my Commander, I replaced the plugs (but they no where near the mileage of needing changed), probably unnecessary, and I'm sure what cured it, was thoroughly cleaning all the electrical connections.
I had the Random Misfire codes on a Chrysler MiniVan and nothing was fixing it either. Multiple times I removed and cleaned the wires and all the connections, only when I took the coil pack out (the 3.3L V6 has a single coil pack for the whole motor) did I find Carbon Tracks on it. I had to take it out twice and clean it thoroughly to get the carbon tracks off and stop the misfires, I probably should have replaced it (and the advice is often to just replace any part with carbon tracks, it burns into the case and you really can't clean it off). But I got it working well again.
For my Mini-van it was winter road salt that got up in the ignition and shorted things out. Once I got it cleaned up, and the resulting carbon tracks from it, the problem went away. For my Commander, I had just douched out the motor from working on the thermostat (I got anti-freeze all over it). I clearly must have gotten water into one of the connectors (dirt or road salt will do the same) that caused the ignition problems, I probably pulled the coil and replaced the plugs for no benefit, I probably just had to pull all the connectors and use electrical cleaner on them.
Oh, Catalytic Converters, you should get a code if they have gone bad. The only way for a Cat to cause stalling and rough running is if they clogged, and if it clogged this would NOT be an intermittent problem. I would look other places other than CAT and if the only code is misfires, I would be concentrating on the ignition first.