This is probably a simple fix once you identify the bad boy. If you have the dealer do it, it is likely a decidedly more expensive fix and will probably consume multiple visits, time, and money with a 50/50 chance of success.
In the end, the dealers frequently give up, pointing out it is not a production vehicle, and the engine package is an enthusiast/hobbyist item they are not well equipped to properly service.
It might be worth contacting FRPP about the issue and soliciting their thoughts, although I suspect that will approximate the dealer's response. Did you get tuning and data logging s/w with the EFI system, and do you know how to use it?
If you received the tuning and data logging s/w, there are a number of excellent online training services that specialize in this sort of education. One I would suggest right off the top of my head is
HP Academy (<=clickable) out of Australia. Take a look, I think you will be impressed.