IIRC the mustang went MAF from VAM in 89 when they went to dual plug heads , there should not be a map sensor
if the EGR is not hooked up then delete it, remove the EGR tube from the manifold to the intake and plug the holes (the upper intake will require you to make a block off plate, extremely easy if you have any kind of skills) if after idling for a few minutes and it acts normal then so be it, if it continues to start to rough idle like you say then you probably either have a problem with your O2 and or computer, either one is cheap to fix (new sensor or a new computer, computers can be had from junkyards for cheap)
remember the EGR only operates at part throttle, so if its effecting idle then the diaphram in it is more then likely shot, removing it and blocking it off will help that issue at idle and WOT, but in all my years messing with the 2.3's ive never had a problem with part throttle ping with the EGR not hooked up
start with the basics listed here already and go from there, then report back with problems