I recently purchased an 89 Mark VII for $600 at auction. The engine is ideal to transplant into a mustang. As you probably already know the HO engine was built really good. 89-92 are roller cam, forged pistons and rods, better flowing heads than the early heads (not saying much).
As far as i can tell they 5.0 never went to mass air on the lincoln mark VII. Just about everything else followed the mustang but in 89 the mustang went to MASS air and the lincoln did not get it. It will cost about $300 on to convert to MASS air. You need the mustang computer. The A9T ($150) from the stick shift mustang is supposed to have better curves than the A9P ($100) from an automatic. Then you need a wiring harness for $25 and you need the intake tube and the sensor itself ($150). Or you can get an aftermarket cool air system but you still need the actual sensor. The MASS error sensor must be matched to the fuel injectors in the car. The JEGS kit should work just fine on a lincoln. The air intake might not have been perfect but so what its not ever going into a lincoln, you would have the same problem with a mustang donor.