3000 RPM is too high........1000 RPM is the target range.
The EFI idle RPM is controlled by the Idle Air Controller (IAC) located on the throttle body. The IAC is a stepper motor driven air passage valve that opens and closes via the EFI controller. It regulates the air flow which simulates the idle adjustment screw on a carb intake system except it automatically changes based on EFI feedback.
If the wiring makes no change then the IAC may be bad, leaky O-ring, sticking due to carbon build-up or a mechanical hang-up.
All EFI parts are available through S&S Cycle.
http://www.sscycle.com/
When you disconnect the battery on an EFI bike, there is a reset proceedure to follow after battery reconnect.
There is a sticker near the battery/fender with the instructions on EFI bikes.
"Connect battery...turn key ON...press RUN button...Allow engine check light to go out...turn OFF key and keep it OFF for minimum of 15 seconds."
This resets all the sensors for the EFI system.
Of coarse you know you loose all learned EFI data when you disconnect the battery. It will relearn it within 50 miles.
Hope this helps.