Thought I would post this in case any other forum members had similar problem.
My neighbor has an 09 Heritage all stock. He had a problem with hard starting (it would crank and crank), sluggish throttle response, occasionally raw fuel would flow out the air cleaner and occasionally it would backfire while starting. After several attempts by the HD tech's they finally discovered that the problem was the crank shaft sensor. Evidently, this screws up the ECM. Fortunately, it was covered by warranty. And all is well again.

Just thought I would post this, in case anyone else might have similar symptoms. This would be one thing to check out before ripping the motor apart. The sensor is located front of the motor down by the oil filter.

 

That's an easy sensor to damage while changing the oil filter. Thanks for the info.