Vacuum leaks will also cause fouled plugs. This is not like a car's intake manifold where one carb feeds all cylinders, and the carbs run richer as the vacuum level goes down while other cylinders pull the crank along. If it has vacuum leak(s) the most-leaky cylinder intake will show the darkest plug.
That said: you haven't mentioned which fuel you are running: it should be Regular or Midgrade with today's fuels, which burn much slower than 1970s gas. That will lighten the plugs, too.
But...this all said: I'm putting my $$ on the ignition. First, like KerryB said, check the plug caps: your OEM versions were 7.5k ohms. If they are more than 8500 now, they are history. Modern ones are 5000 ohms for this engine, so in the end you may wish to run resistor plugs like the DR7EA instead of the D7EA or anything colder, along with the 5k plug caps, to get a long-enough spark to help. However, the Dyna S makes for a very short spark, even with stock coils, and if you have the 3-ohm coils that bike will not support them, as it cannot make enough electrical power to feed that ignition system. At the very least, you will need to fix up the coil situation if yours has those.
