Shortly after buying my 08 FI Road Star, I noticed my back plugs were fouling. It caused rough running at first, then fouled plugs. I thought it was bad O2 sensors, then I thought it was faulty or plugged Fuel Injectors. Maybe bad coils?
What it turned out to be was the Vacuum line that runs from the "Air Intake Pressure Sensor" to in Intake manifold air nipple, right on top of the intake manifold. (right between the injectors). The sensor is under your Gas tank, front left side.
Where the Vacuum line attaches to the nipple, had swollen and gotten soft, then developed a split down the side and eventually broke off. This lack of vacuum signal made the injectors run extremely rich.
I replaced the Vacuum tubing with some Silicone Vacuum tubing from NAPA, 5/32" or 4mm. I rerouted the new line in a gentle curve so as not to kink. I think all the other wire bundles that were laying on top of this hose it what caused the damage.
This very simple $3 repair requires removing of the fuel tank completely. You cannot see either end of the hose or sensor with the tank still on. When I removed mine it was easy to see the intake end was damaged (swollen and soft) from it's close proximity to fuel.
If your are running a FI bike I recommend changing out this hose next time you have your tank off. It only takes a tiny amount of air slipping through to make your wonderful bike to run crappy.
Don't just pull your tank and look at the hose, take it off and just replace it, you won't believe the difference it makes, even when the damage is slight.