no spark cylinder #3

Swap a trigger coil?  Balance the carbs? 

The carbs are already balanaced with a carb mate and I doubt it is a carb problem because when it is running rough pulling the choke has almost no affect.  Also, I am fairly confident in my low EGT reading on the #3 cylinder.  After shutdown the exhaust on that cylinder is noticebly cooler.  I am also confident in my timing light and have double checked that so I know that when it is running rough I am not getting a spark to #3.  Whats the best way to swap a trigger coil?  Do I switch physical position and then the pin position in the 6-way?  I have looked at the gap on the trigger coil and it is not really that adjustable but have it set pretty close to the .012.

When you say that it runs very rough and there is no spark on #3 then I assume that the timing light shows no spark on either the top or bottom plugs. Failure of a single spark in a cylinder is unlikely to give very rough running.

It is unlikely that you have a problem with 2 separate ignition systems. There shouldn't be any common mode failures of the ignition that give the symptoms that you describe. It could be that there was a single failure on one system some time ago and this wasn't noticed and then a second fault has developed with the second ignition system and now it is noticeable.

I would use the diagram and resistance values published in the heavy maintenance manual and measure the resistance with a multimeter from the 6-pin connectors. Whilst doing this, pull on the various wiring harnesses to see if the resistance changes indicating a break somewhere.

Let us know what you find.

Try replacing the spark plugs. Even if they test okay they can still be faulty. I’ve had brand new plugs that were defective right out of the box.

Did some more troubleshooting today with no resolution.  Switched spark plugs and caps for cylinder #3 with cylinder #1.  I then removed trigger coil assembly and tested coils all the way to 6-way plug.  Also took trigger switches apart and found fair amount of oil in the switch, cleaned out and everything else looked good.  I wrongly stated no spark to cylinder #3 as I am still getting spark to bottom plug.  When I reinstalled trigger coils I had problem adjusting the gap for the B3/B4 coil.  This is the coil that fires the top #3 plug.  When one flag on flywheel comes around I can gap to .012 but when the 2nd flag comes around the closest gap i can adjust is .025.  I can not see any damage or wear marks on the trigger coils or the flywheel.  I need to recheck the gap in the other trigger coils but I beleive they are good.  I potentially know why cylinder #3 is not firing but still do not know why it alternates between running rough and smooth.  I also am not sure that buying a new trigger coil is going to allow me to adjust gap to .012.  I am also wondering if my crank is not straight.