Sounds like it may be the engine temp. sensor to me. Making the bike think it never warms up and running rich in warm up mode. Have you checked for diagnostic codes?
I agree with wildspirit here. The black plugs are telling you that too much fuel is being sent to the engine. Possible cause is the engine temp sensor on the rear of the front cylinder head.
Check for codes.
04-07 HD DTC Codes and Activation - Harley Davidson Community (04-07 HD DTC Codes and Activation)