Fatboy starts runs for about 25-30 minutes then coughs and splutters, then runs on half power. Once cooled down will run for 20 -30 minutes again-- checked plugs and wiring as well as possible. Help

Carb or Fuel injected? (what year). You have something getting hot and malfunctioning... either the ECU (fuel injected) or the ingnition control module (possible on either)

Sounds like something in the ignition is overheating and breaking down. Maybe it's time to take it to the dealer.