If I recall, you have the 6+6 connectors.
The Trig Coil and the Mag switch are on the same connector.
When you swapped connections you also swapped Switches.
If the T-Coil was bad it would remain associated with the same switch. No apparent Change.
Since the Problem DID swap, The problem is AFTER the connector. I-Modules, I-Coils, Plugs, Wiring.
The EGT probe is NOT on cylinder 1+3, It is Either 1 OR 3, I will assume #3, Or commonly Both rear Cylinders, (2+3)
Sooty plug at idle is not uncommon.
Why #3 is clean is the question.
You are seeing #3s EGT go HOT during the misfire.
This could be because the unburnt fuel get ignited in the exhaust pipe and back-flashes into the cylinder burning the soot off of the plug.
- - -
Just to confirm we are on the same page...
Does this miss-firing issue only occur when operating with Mag-B ON and Mag-A OFF ???
- - -
The problem appears to be associated with only the #3 "B" (Top) plug. Very Strange!!!
To rule out the Plugs...
Do not Replace the plugs, but Swap the plugs in Cylinder #1Top with #3Top,... and #1Bottom With #3 Bottom just to be inclusive.
If the problem moves to "A", suspect the now #1 Top Spark Plug.