The manual I have shows only one pulse generator for 1997 and up.
So if you only have one, that eliminates that as causing one cylinder failing.
It would feed signals for both to the ICM.
You did say all plugs are getting spark so ignition is not causing it. Unless one is weak.
Maybe the flooded plugs. Possible compression check would be good to know.
Here is an idea, shut off the fuel supply and drain the carb bowls by loosing the drain screw on the bottom.
Clean the plugs and dry them, crank it with no fuel supply, and spray a little starting fluid into the carb with the dead cylinder. If it fires that means the ignition and compression is fine. Then go after a carb issue.
This is a handy tool to see how strong the coil is. You can be put at the end of both plug wires on one coil, and open it up to see how much voltage is being produced. Maybe a local auto parts store will have them.
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