1996 200hp vindacator ignition problems

I am having weired ignition problems with my 1996 200hp vindacator. It was not getting fire on the #2 cylinder a service tech told to disconnect the harness to isolate the problem from the controls. I did that it started getting fire. Plugged the harness back and still was getting fire. The next day I checked it same problem but not only the #2 cylinder but now the #3 cylinder also. I changed power pack and switched coils around and still getting no fire on those two cylinders. What am I missing?

If you disconnected the harness and you get all cylinders fire, then your harness has an intermittent problem; probably key ignition itself. It's not always there. I would leave the harness to the control off, have the kill wire at the pack ready to ground it and shut the engine off when wanted to, use the timing light to detect spark on all plug wires while it's running. If they all are firing, then surely you have a problem with the key ignition or somewhere in the harness to the control.
While having an intermittent, you went change the pack and coils. It wouldn't help.