I am just reading to learn about EFI tuning and have come across something called Alpha-N (throttle angle-engine speed) algorithms to estimate engine load because it worked better on Stacked type intake with individual throttle bodies, when no common intake plenum is available for monitoring. Because large pressure changes with small throttle movement and since the pressure changes happen over small throttle angle the idle vacuum is less than on plenum manifolds. So that means its harder to get a solid MAP reading even when tubing or hose is connected to each chamber each pulse feeds a strong signal to MAP giving you a noisy signal. The Alpha-N algorithm uses throttle position to estimate engine loads and makes it work well.
-This info is taken out of "Designing and Tuning High Perfromance Fuel Injection Systems" by Greg Banish.
I'm still reading so I don't know if any of the MS's are capable of this algorithm but it for what it's worth it maybe that is why your chasing idle using MAP inputs on MS2, I was interested in ITB for my 2.8L N/A so I'm doing as much reading as I can between that and MS to properly understand how it works so that I can plan ahead.