I'm going to drop a reasonably long post. Hopefully this really helps. First and foremost, if you need a stock computer that is correctly refurbed or want somebody to repair yours, you need to contact Josh Popper with Encore Mustang Parts Warehouse.
Stock Computer/Moates QuarterHorse - The stock mass air fox body computer is EXTREMELY capable for tuning the vast majority of bolt-on fox body combos... including N/A, Turbo, and Blower. Nitrous can be done, but generally a standalone controller is a better way to go... depends on the size of the shot and whether you are doing a dry/wet kit, and how much control you need of the nitrous itself. But for this to work well, you need a quarterhorse chip and somebody that can teach you how this stuff works. I've been slowly working on a collection of youtube videos teaching how to do this stuff, and work with new users every single day to teach and help them tune their cars. I'll also gladly extend the same offer to you if you are interested (it seems like you are). You'll need a wideband, a quarterhorse, and Binary Editor software. Ben Head at Core Tuning can provide everything you need, including the wideband, if you want to go that route and buy everything new. I also see guys from time to time sell off a complete quarterhorse/binary editor package on the cheap as they change direction or sell the car. Look around on some of the facebook groups for fox mustangs or binary editor, along with thee and other forums. You'll likely find something pretty quickly. Shoot me a message if you want to get on the phone and talk more about this route.
Holley Terminator X - The Holley system, as another member stated, can be a suitable option for people that are currently carbed or are starting from nothing and want to go to EFI. This is because it's going to come with all the harnesses, the computer, etc. So essentially, if you're starting a project where you don't already have any of that stuff, and would have to source a computer, harness, and sensors anyway, this is arguably an easier path. A word of caution though... don't get caught up in the hype of Auto-Tuning. I see way too many people suggest going with Holley because "you can know nothing about tuning and just plug it in and it will magically tune itself". That's largely BS. Yes, some aspects of the tune will self-learn to a degree within a range of error. But it's never going to be perfect. If you don't know how to tune EFI systems, and don't really want to learn, be prepared to get poor or average results out of a self-tuning system. The Holley software is pretty simple to use and learn, which is nice if you are a new to tuning, but you may get frustrated later on by the lack of granularity in certain portions of the tune, when compared with other options. Really seems like Holley is trying to generalize and simplify things as much as possible for users. The Holley does have some nice features, but in certain combos, you may not need most of them. I don't see where you've listed or anyone has asked any specifics of your combo. So IMO it's a little absurd to blindly recommend any one system just cause of a feature set. If you're naturally aspirated, and don't track your car a bunch, I just don't see the benefit of going this route. And truthfully, even if you have a blower on the car, not a TON of benefits there either. Now turbo and nitrous is where this is going to shine when compared to the stock computer. Just a thought. Please share more details about the combo and direction you want to go with the car.
Megasquirt - These systems are a good option for those who generally have a solid wiring harness in place already, but have a failing or no stock computer. This can be purchased as a plug and play system and leverages a MAP sensor to facilitate speed density tuning... that means no MAF. That could save you costs in the future if you go through multiple combo changes that require new, bigger MAFs. But at the same time, the initial investment in the system compared to a stock computer setup is a little out of line. And like the Holley, if you have a simple combo, many of the features in this system may not be of much use to you. The software interface here will not seem as modern or simple to you. But there is a lot of granularity here. Just to prove a simple point, the instruction manual for the Holley software is 39 pages long, compared to the MS manual at 207 pages. There are different manuals for different versions, but you get the idea. The MS setup is very packed with capabilities, but again, simple combos aren't likely to benefit from many of them.
So in summary, figure out the condition of your computer and harness, decide what you really want to do with the car, and find a mentor willing to help you through the process and is familiar with these cars and the tuning setup you want to use. To a certain degree, not vastly different than just getting your car professionally tuned. You would always want to go with somebody that knows the type of combo very well, and the particular computer management system and other hardware you are using. When in doubt, always ask the tuner what they prefer. Certain injectors, MAFs, ECU, widebands, etc. A good tuner working with
they're unfamiliar with and is poorly documented will generally not lead to the best results. Again, feel free to message me any time if you'd like to talk. Just here to help. Cheers. -Matt