I want to go fuel injected

greyfox69 wants to convert his 88 5.0 to carb. PM him and tell him what you know about your carb experience. Maybe you can trade carb parts for EFI parts...

The 4 cylinder wiring harness won't work. It is very different form the 8 cylinder wiring harness.

Mass Air EFI systems are more adaptable to various engine modes without argument from the computer. For that reason, I would recommend a Mass Air conversion.

Mass Air computer will be an A9L or A3M (5 speed).
An A9P (auto trans) will work if you can't find anything else.

You have 5 wiring harness options:
89 Mustang 5.0 harness for a Mass air setup.

Ford Racing Mass Air conversion harness M-12071-A50* $575 at Summit Ford Racing M-12071-A50 - Ford Racing Multiport EFI Wiring Harness Systems - Overview - SummitRacing.com

Ford Fuel Injection Mass Air conversion harness See Ford Fuel Injection » Wiring Harnesses and RJM Injection Tech — Welcome harness is $550
Lots of good information on the two sites above. They have a page that tells you all the parts you will need besides the wiring harness.

Junkyard 86-88 5.0 Mustang Speed Density - can be converted to Mass Air with an additional adapter wiring harness. Or you can use is as is for Speed Density.

You will need a different distributor, fuel pump, fuel pressure regulator and fuel lines. You may benefit by buying a wrecked 5.0 EFI Mustang and stripping it for parts. Check with the insurance companies: they sell the wrecked cars for a very cheap price. Some will go for $250-$400. Sell the shell for scrap once you have stripped and sold all the usable parts.

Im in the process of doing this haha. Here is the parts I have collected to swap my 1980 over to efi..

Computer harness out of an 89
Fuel injector harness
02 sensor harness out of a manual trans car
Full body harness out of an 89 GT
140 speedo out of an 89
Black dash and center console
Gas tank with efi fuel pump

I still need...

Intake manifold set
computer
all the various engine sensors
02 sensor bungs welded into my headers
throttle body and spacer
fuel injectors with matching maf

Im sure im forgettin something but that's the majority of it..

There is a lot involved, but it will be worth it when its all done