I've been there too. in fact, my badly running EFI system took a cylinder and two years of my life with it! That was after spending thousands of dollars with the local EFI expert, trying to make it run properly. The "expert" wasn't. They just tried to fix it like I did; through trial and error. They didn't have a clue. All they could do was replace parts, play with settings and cross their fingers. Sure, they knew enough to install it but when it went bad, they didn't have the equipment or the technical knowledge to diagnose the problem.
I finally began calling around to manufacturers like Roush and Kinsler, looking for advice. I was referred to Autotrend EFI in Northern California. I live in Vancouver but was so fed-up with EFI, I decided to ship my Pantera there on the chance they could solve the problem. The first thing they did was to connect a laptop between all the sensors and the ECU. They also had a laptop connected to the ECU with the tuning software running on it. They started the engine and immediately noticed the dual sync distributor was not sending the cam sync signal when it should. It was sending a signal but not at the right time. If it had not sent any signal or the unit had failed completely, it would have thrown an error code but since it was sending a signal, there was no error. They replaced the circuit board in the distributor, fired it up and it ran like it never had before...perfectly. I didn't know whether to laugh or scream!!! The whole process took about 30 minutes. They spent another 30 minutes fine tuning the calibration and finally, I had what I'd always wanted. Unfortunately, I started looking at Panteras with individual runner systems and couldn't resist!!!
Later on, they told me they had a feeling my problem was the distributor the first time they spoke with me. Apparently, my particular dual sync distributor has about a 50% failure rate! That's why they had a spare circuit board on hand. Funny, when I spoke to the manufacturer's tech support, they never suggested that might be the problem!
The moral of the story is, don't buy your EFI system from Summit , Jeg's or Amazon because you want to save a hundred bucks. Buy it from a dealer who's truly knowledgeable. You'll get the same price as Summit, Jeg's or Amazon but you'll also get someone you can call when you have a problem. Someone who truly understands your system. Don't count on the manufacturer's tech support. It usually isn't very good, if you can get through at all. Besides, don't problems always happen on the weekends? Hey, I've got my EFI dealer's cel. phone number. I can get help on weekends and holidays!!!