no spark cylinder #3

The gap will set the amplitude of the trigger signal to the SMD module. The amplitude also increases with engine speed. At cranking speeds the amplitude is low and this feature is used by the SMD to trigger off the trailing edge of the 'flag' to give retarded ignition timing to aid starting. At normal running speeds the amplitude is higher and the leading edge of the 'flag' is used to give advanced ignition timing.

If the output from the trigger coil is low at running speeds then it might be possible for the incorrect timing to be selected. If it is below the minimum threshold for the 'starting circuit' then there will be no spark.

If you have achieved a correct gap on one of the 'flags' then even if the other one were far too large you would expect at least one spark in every two to be present. Your timing light would have shown a more intermittent spark if this were the case.

There is one other possibility, that you might have a shorted-turn in the trigger coil. It is still possible to have approximately the correct resistance but if you measured the inductance it would be very different to the others and is likely to produce a much smaller signal.

Can you swap the trigger coil in question with one of the others and swap over the corresponding pins on the 6-pin connector. If the fault moves to the new cylinder then the problem is with the suspect trigger coil and you replace it with a new one knowing that it will fix your problem (assuming that there isn't an intermittent problem with the wiring or connector).

Thanks to everyone's thoughts I am definitely getting closer.  I modifed the mount just a bit for the B3/B4 trigger and am now able to get gap at .012.  I now have good ignition and engine ran great with spark to all cylinders, fairly even EGT's and minimal drop during mag check.  I thought everything was good until I moved on to the carb balance.  During the first throttle adjustment the engine started running very rough again.  During first engine run I had noticed that the float bowls overfilled but had thought it was due to rough running engine bouncing floats around.  However, today I noticed when it ran rough only the right side float overfilled.  Since the #3 cylinder is closest to the carb I am thinking some of my problems are carb related.  I have new floats but weighed them again and the heaviest set weights 6.2.  I then checked the float arm adjustment and it is correct.  I have new float valves but removed them to check for debries and found none.  However, when looking at the seat for the float valve it looks to have machine marks and is not a very even surface.  Is it possible the float valve does not seat real good and when the motor starts running rough, the bowl overfills creating an excessive rich mixture?  If this is the cause what is the fix? 

Yes the needle valve seat can cause flooding and rough running. There have been a few instances where I had to polish them and smooth them out to make a good seal.

any tips on getting this done?  I am thinking I can use my old float valve to get the right angle - would I use some beginning grit aluminum polish on the end?

You’re not trying to change the angle inside this area, but just polish what is there. If the angle for the seat gets changed then your buying a new carb. Use a light brass / copper polish. I then take a 6” Q-Tip and break off the stick part until it’s about 2” - 2.5” long. I put the stick end in a small drill. Then I cut a very small piece of cloth in a round shape to go over the tip of the Q-Tip. I apply the polish to the cloth and insert it into the seat area to the bottom. I only use the drill on slow speed. I just use the drill because it is far easier than turning the Q-Tip by hand. Just run it slowly and let the polish do its job. I sometimes do this three times. Remember we don’t want to damage the seat surface just polish, clean and smooth the seat surface. 
So far I’ve had good success doing these.