I would think something is not right if an EFI system is cranking for 3 seconds before starting. I've also never heard of the rough idle issue like this before. If it was all that common, I figure we'd have a number of people posting to ask about it after installing their kits.
Well, at least mine starts right up LOL

As for the "temporary slightly rough idle after initial start up flair", I have two theories:
1) I need to drill the hole in the throttle plate slightly larger to allow more airflow into the throttle body while the throttle plate is closed then what the IAC is allowing. If you slightly press the open the throttle plate during the rough idle, it instantly goes away. It could be "starving" for air
2) Maybe the regulator on the fuel rail is leaking down slightly when the vehicle is shut off

I don;t think this is the issue, as the fuel pressure checks out OK at the rail, and it starts up very easy.
It usually only does the rough idle on a cold start. But, sometimes it will do it on a hot restart after long highway driving. But, after the 20 or so seconds of rough idle, it magically clears up, like it is possessed
I had reported my issues on the Hesco sight, and they kind of offered some help. Now, they wont let my posts show up or answer my last question

Last response I got was "you installed it wrong"

They might have got mad at me because i commented how my "factory computer controlled BBD Carb equipped 83 Scrambler starts up better then my fuel injected one"
I have went back and double checked my entire installation, step by step per the Hesco/Mopar instruction manual, everything is correct. Intake/exhaust manifold bolts still tight, all fuel line clamps still tight, distributor installed correctly, etc, etc, etc.
The only thing I can figure is the IAC issue. That is what the Hesco people seem to think. I have hooked the diagnostic port up to three different scan tools and I have no codes
