The 1988 460 truck EFI distributor is a bolt-on.
The 1988-1993 Mustang 5.0L harness (or the aftermarket harnesses) is a bolt-on, with deletions because it contains a lot of stuff you won't need/use. The computer (PCM) is also a bolt-on.
The intake manifold will be a carb manifold with injector bung modifications and an aftermarket intake elbow/throttle body bolted up top where the carburetor used to sit.
Look at my stuff. http://www.racesystems.com/cobra
Fuel rails can come from Probe Industries or anyone else that makes retrofit rails for 460 Carbureted manifolds, or you can buy fuel rail stock and machine it yourself.
Air meter (tells the computer how much air mass is entering the engine) comes from a variety of places depending on the power you're going to make.
Fuel injectors come from a variety of sources again depending on the build and power level.
Sensors come from Ford.
Fuel pump comes from a variety of places, like Weldon Racing, etc...depending on your goal/needs.
Lastly, you buy a tweecer. www.tweecer.com
to reprogram the computer for your engine displacement, injector size, injector firing sequence, and whatever else you need.
Basically, just pretend it's a big 5.0L Ford, plug it all together, and tune it with the Tweecer. And if you need a part, the Ford dealer has them.
Take a look at this for rails and bungs...and the required manifold mods.
The intake elbow you choose must clear the hood, flow enough, and have provision for a Ford IAC valve. I made my own. Are you a CNC machinist? I designed mine in Solidworks.