I’ve ironed out various teething problems I've had with the setup of my EFI, and now am left with just one. It seems like it’s the same issue you faced.
I’ve set the timing control via the Sniper EFI, and like you, I'm running a MSD distributor.
The car runs beautifully above 2000 RPM and the timing sticks right where it's supposed to, at revs above 2000.

Unfortunately, at idle the timing looks to be VERY erratic. Hunting anywhere from 7°-30°, although tending to be closer to the targeted 15°.
Idle RPM isn’t as smooth as it should be, and it smells rich.
I’m at a bit of a loss really. Was your issue fixed simply by reinstalling a fresh setup?