an intake cough is a symptom of a LEAN MIS-FIRE.
in MM injected bikes, the causes may be leaky intake seals or a problem with the engine temperature sensor.
both are common problems.
to determine if the problem is leaky intake seals, spray carb cleaner on the intake seals with the engine at idle. you will know right away if you have leaky seals.
if not leaky seals, then I would consider replacing the engine temperature sensor. it is located in the front head sticking straight up through the center of the rocker cover. you don't have to remove the fuel tanks to change it out, but I would suggest you do that if you decide to replace it.
- note: HD no longer supports your EFI system. your best bet, for ease of maintenance and long term reliability is to strip the fuel injection and replace it with a carburetor and standard EVO ignition.
if you are considering this option, let me know and I will provide more detail.