Sorry, I never took the time to read your mods. You probably do need to convert to mass air, those computers are very picky. In the mean time you could try and mess with the idle to see if it helps.
I have this happen on occasion to mine, however, I have an aftermarket camshaft in the engine so the computers always trying to "hunt" for the proper idle and in doing so, bounces up and down until I straighten it out with a push to the gas pedal.