Sounds like it might be the Throttle Position Sensor either out of adjustment or bad. Not sure what ECM you have on that bike but if it is the S&S you can pull the trouble codes with Pro Tune Software and that will tell you where the issue lies.
Glad to help, let us know how it goes. Don't hesitate to ask if you have more questions. The Manual has a procedure for adjusting the TPS, that might get you going.
I'm just hear for the beers, I never had the privilege of owning an EFI. When you replaced the pump, regulator and filter did you notice a crack in the housing that holds the regulator that would cause a leak in your tank?
