I had a very similair frustrating experience, granted it was a 93 t-Bird Super Coupe and it WAS a Mass air car. I changed SOOO many parts and took it to many shops, one of which was a Ford electronics expert and nothing!
I decided to sell the car after 7 yrs of ownership, it was just getting too old and problematic after while, anyway, the guy who bought it was a hotrod builder and he spoke to a friend that had a Super Coupe and told him what to do to get the car running.
it WAS A VACUM LEAK
Everything looked tight and you dint hear the leak anywhere but the steel collor that attached to the intake plenum coming from the intercooler. The guy took a screw driver and a rubber mallet and slammed the collor as hard a s he could a few time, the Car started right up and ran like a champ but i had already signed the title.
Check for any places where there potentially could be a leak and get them really tight. Usually when issues like this are bieng so difficult its a simple thing that gets overlooked.
Good Luck