On another post I suggested that one of my favorite tools is a blown up copy of the electrical diagram and then laminating it. Then you can mark up the diagram every time you come across a connection and check it . Also if you have an update to your wiring, you need to update your electrical diagram and understand what you've got and what to expect when checking/testing.
Prime example is your previous comment on finding a black wire , green wire , and a blue wire not connected ??? then figuring out that that was the previous primary feeds to the coils.
Bottom line, your Dyna system should have a clean feed of full battery voltage going to it and a clean ground after it. What the Dyna ignition feeds to the coils is part of the Dyna system design and I'm not sure if you can get your hands on the installation manual for the Dyna system, but it would help in diagnosis. Sometimes manufacturers have that info available online as a download.
Just went to the Dyna site and they do have downloads available for all their products under their support page
www.dynaonline.com/skins/products/harley_davidson/dyna_2000/ 
