In order to put an M90 on the car you are going to pretty much have to swap the entire engine. There are many small differences between a standard single port 3.8L and a M90 charged single port.
The M90 engines also have forged parts in them, so they are more desirable that way as well.
If you can get the whole Cougar for a donor car. Do it.
1990 Lincoln Mark VII 5.0 HO 5-Speed Swap- BBK O/R H, Hooker Max Flows dumped, coil conversion
2012 Fiesta S 1.6 5-Speed- 40mpg
Past: 89 Hatch, 89 Notch, 01 V6