wow... where do I start.
first off, both engines have a 5.0L displacement. CV/GM/TC engines are standard output motors. Mustang and Mark 7 motors are High output motors.
HO motor uses the 351W ignition firing order. SO CV motor uses conventinal 289/302 firing order.
the block, crank and connecting rods are the same. CV motor gets cast, slightly dished pistons. HO motor gets Forged flat top pistons with valve reliefs. ALL 5.0L passenger car engines use hydraulic roller cam starting in 1986. HO cam is much more agressive with 266 duration and .444" lift. CV cam has 240/250 duration and .379" lift. for more info on cams, read here; 5.0 truck cam
HO motors use a different exhaust also. typically a factory style stamped shorty header with a 2.25" exhaust outlet and dual exhaust. CV motors use iron manifolds with a 2" outlet and dual exhaust was optional.
87 up HO motor uses E7TE cylinder heads. these have an open style, 64cc combustion chamber, which flows better compared to the close/swirl style 69cc combustion chamber on the E6SE heads used on the 86 HO and 86-91 standard output motors.
both motors use SEFI fuel injection (sequential electronic fuel injection) but the HO motor uses 19lb (orange) fuel injectors and the SO motor uses 14lb (grey) fuel injectors.
the EFI Lower intake is the same between the 2 motors. the upper air plenum/intake on the HO Motor is larger (63mm inlet) than the SO motor (53mm inlet). Of couse this means the throttle bodies are corresponding sizes also, 60mm on the HO (1987 and up) 50mm on the SO motor.
The ECM's between the 2 are different too, HO ECM is more aggressive and the fuel map is much different because of the cam and larger injectors.
You can swap the HO cam in the SO CV motor, but it requires you change the ignition firing order, install 19lb injectors and run an HO ECM.
Mark 7 ECM is the best in the CV/GM as 88 and up CV/GM uses an intergral cruise control system that is defeated if you run a Mustang ECM.
you can also swap to MAF but it requires the motor is convert to HO(cam and injectors) and run a Mustang MAF ECM.
mark 7's were never equipped with MAF, so you wont find an ECM there.
I hear 91-93 HO T-bird/Cougar MAF ECM's will work, but never tried it.