OP, as you begin to investigate EFI systems some of the attractive points you will find for the aftermarket systems will be engine protections for low
oil pressure, fuel pressure, lean conditions etc and traction control systems. The first protection systems I mentioned will protect your engine the last one protects you. These cars can swap ends so fast you didn't realize what was or did happen. The traction control can save you and your car. It will not turn it into a docile DD but it will make it more difficult but, and this is important, not impossible to loose control of.
An additional consideration is the engine wiring harness. Aftermarket systems usually (almost always) require you to build a wiring harness. The system I will suggest allows you to use an existing wiring harness off an OEM vehicle. The benefit to the OEM harness is you don't have to build it and it is the most durable harness typically available. They can be inexpensively sourced from a salvage yard and here is the best one — they are plug an play with the right EFI system.
The challenge with the aftermarket EFI systems is that the good ones that do all this stuff will end up costing you ~$6K or more by the time you are done. I am going to suggest an aftermarket alternative that is much more price friendly. You should know before you read the recommendation that I am prejudiced (in a positive manner) about the particular system. There are may systems outer there that can do some of the things this system I'll suggest can do and others that can do all of the things this system can do but there are no systems that can do it as inexpensively.
The system is the MegaSquirt3 Pro Plug and Play EFI. Click here =>
MS3Pro PnP to jump to the product page. It will work with the Ford OEM wiring harness for a 99-04 Ford Mustang 2,3, or 4 valve. If you use a pushrod engine then shut off the OHC stuff in the tune file and tune it as a 5.0 L engine. An extra added attraction is the system uses all Ford OEM sensors so you don't get ripped off for pricey aftermarket sensors that if you knew the brand name of could be obtained for pennies on the dollar.
The included tuning s/w is unusually flexible and will handle virtually any type of ignition, fuel system and injector selection you may want to use. It will support a speed density or MAF based fueling model which will be more meaningful to you as you dig into the project. The $1,350 purchase price includes both the tuning and dataloging s/w. If you use a MAF based system once tuned you can go anywhere with the car. If you use a speed density you can go most places. Significant altitude changes or significant atmospheric changes will require some tuning massage.
This next step is a big deal. If your state requires you to pass emissions with the vehicle it doesn't matter if you are carbureted or injected you have 40 miles of bad road before you. If your state has a smog exemption program for replicas find out the program name and register the car under that program irrespective of which fueling model you pursue — your life will be simpler and much easier.
Ed