The larger 70 MAF housing was standard on the later years of the 3.8 and 4.6 IIRC (94-97). The 91-93 3.8 mn12s IIRC use a smaller 55mm MAF housing. It runs a bit better with the 70mm housing and doesn't stumble/hesitate when cold anymore in drive. It is a bit better in reverse now as well, it doesn't stumble in reverse or stall as easily as it did before but the RPMS still drop low in reverse causing a stall once in a while.
Although the MAF housing now that I think of it might explain the variance in gas mileage. I'll have to see how both compare. I figured it wouldn't make much of a difference since it is an early mass air system but maybe that combined with no air silencer (stock airbox though) is causing a problem?
It's might not be a bad IAC, thanks for mentioning that sound as I remember now what it sounds like as I had a Grand Marquis that had the IAC fail on it which made that sound. Not sure about the whine, it happens so quickly that by the time I open the hood, it's often already gone. It might be just normal power steering whine under load (it happens when it's being reversed to park on a hill) if that's typical of Fords.
I'm not sure why you believe using the original sensor in a larger housing is supposed to help things without tuning for the difference in air.
A MAF sensor reports a difference in voltage based on how much air flow cools the heated wire and changes the voltage. The MAF transfer function in the ECU is calibrated because they know that at a certain CFM, XXX cu-ft of air is let in.
By changing the diameter of the housing, you are in effect changing the amount of air being let into the engine for a given reported voltage. That transfer function is now out of sync with reality so hillarity ensues. Had you switched ECUs and the entire MAF at the same time, you probably wouldn't have these drivability issues (but you would need to confirm that no other functions are being left out and/or not accounted for by comparing pinouts. Ex: 95-97 ECUs also controlled the transmission and won't be happy if that's missing).
I suspect you are seeing a hesitation at idle because your idle air control valve (IACV) is gunked up and/or not working. When cold and at idle, the IACV is supposed to open up to let more air into the engine and keep it rev'd up more to warm things up.
Now, my theory doesn't completely explain why you claim the engine is better at idle when cold and you have the frankenMAF hooked up because when the throttle body is closed, I wouldn't expect that much more air to flow through the pinholes in the throttle plate.
As far as drivability is concerned from your original post, my first suspect would be the O2 sensors. Have they ever been replaced? O2 sensors degrade over time and that's often a key reason higher mileage cars start seeing a drop off in fuel economy.