I did some more inspection/troubleshooting today...with no conclusions
Initial start up all 4 cylinders were firing.
Battery voltage is at 12.95vdc
Wire harness and connectors look great.
The spark plug wire boots at the coil (#2/#3) appear to be touching the top of the motor so I thought perhaps I have an arcing problem. I rerouted the wires and started the motor, still have spark on all 4 cylinders.
While futzing around the motor started to idle a little rough, I thought it was fuel starved since the gas tank was off, so I put the tank back on and started the motor again to see how it goes, #2/#3 are dead!
Great! Now I can isolate the problem!! I started wiggling the wire harness, the plug wires, the wires going into the Dyna S...nothing changes!
I pulled the tank back off to see if it possibly has something to do with it and nothing changed.
I took a lunch break and thought I'd grab some new spark plugs to throw in just to see it's effect.
I get back to the bike, put the gas tank back on to fill up the float bowls, hit the start switch and the motor is firing on all 4 cylinders again! Argh!!
While it was running I unplugged the yellow wire going to the #2/#3 coil and of course it started to run like crap again and died. Plug the yellow wire back in and it is still no spark on #2/#3.
So I may have just killed my Dyna ignition....hopefully that really was the problem this whole time.
If I had any hair on my head I surely would have pulled it all out trying to troubleshoot this.