Sorry that this has not been an easy fix so far. I see variations in my idle kph just due to changes in atmospheric pressure I suppose it's not a big difference from 30 to 36kpa at idle.
I run two different boards and everytime something is wrong and I swear its the MS unit itself......I swap it and the identical symptoms appear on the other one. It always seems to be something external. (though the 3.57 board is much cleaner regarding noise) For the money, if you can't chase this down I would by a stim if you do not have one. If the MS board is responsive on the stim with different inputs and reads normal atmospheric kpa then I would trust it.
Just curious, is your car still running poorly at mid rpms? or is this just at idle right now?