I just put this exact engine into my '87 Mustang.
To answer your questions for a Cobra:
The front cover is ok unless you want to use a mechanical pump, then you'll have to change to an older style.
The water pump is a Mustang serpentine reverse-flow type. You'll need to change that.
No pulleys come w/this engine. The balancer is std '82-up small block 50-oz imbalance. Put on your pulleys and go.
The
oil pan should work. It's a std Fox Mustang rear sump with a left (driver's) side dipstick.
The flywheel should work fine and a std Mustang clutch will fit.
Bellhousing can be late Mustang or aftermarket scatter shield.
Intake/carb will fit. Distributor must have a bronze gear to fit the roller cam.
This is a great little engine for the price. Make sure you get the latest version that has the roller rockers and aluminum valve covers.