Were the new coils a close match for resistance on the input side to the OEM coils? If the resistance is too low, they will overheat from excessive current -- only option is to replace them.
The DynaS ignition system may put out more power (current/amperes) than what the coils are rated for (that pesky input resistance thing again...). Are all of the parts rated to work together?
Have you measured the voltage across the battery terminals, with the bike running, to make certain it is below 15 Volts? New parts which are defective, occasionally slip through quality control, to the customer's hands.
Bottom line is that if the coils have been smoking, they are damaged, and they need to be replaced. They consist of coils of wire, wrapped around an iron core. The wires are coated with a thin layer of varnish insulation. Once that insulation burns, you have shorted coils, which reduces the function, if it works at all. The shorted coils could burn out the rest of the system, as well. Cheers!
1979 CB750K (sold, 2012, but not forgotten)
1983 Kawasaki 440 LTD Belt Drive (sold, 2011)
1993 Kawasaki Voyager XII