Need input- ECM ?
Got my tank back from paint, 06 low rider installed parts from old tank 09 fxd ,to painted tank. ,cut wires to idiot lights ,to relocate, same for fuel gauge. Installed handle bar top clamp, Got everything wired, went to connect neg. post back on batt. in my haste to get the bike ready for a run the next day I forgot to disconnect neg. cable, Now the bike runs like crap, sometime it idles then it doesnt , cuts out at speed , then its allright, alot of decel pop . ECM ?
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Possibly ECM but there are other possibilities, such as a fuel pressure issue being as you were in that area. I would have it properly diagnosed before you have an expensive new ECM and other parts and still have the problem.

 

Sorry to hear about the problem. all i can say is to take it to a shop and as Geargrinder states get it diagnosed. This is a reason that EFI sucks. you cant work on it yourself. You have to pay, pay and pay some more.

 

Try a thunder max EFI I have one on both me Harleys and love them the Thunder MAX EFI is the best up grade I have ever made no more prob and the down loads are free. My bikes have never run better