Hi Sam, well I'm a computer geek at heart so I'm a big fan of the stock computer. With a little time and effort, as well as a chip and tuning software, you can do all of the tweaks (and many many more) you might make to a carb from a laptop without ever turning a wrench / screwdriver or buying parts / jets / gaskets / etc. It's a far more powerful computer than the Fox unit, and if the parameter exists, you can tune it (shift points, mixtures, pump shots, power valve settings, you name it). My '95 runs a turbo, stock computer, self-tuned, though I only hit the track as an amateur. I have hit the high-11's, I'm not going to try for more until the kids are grown and I get a cage.
I also grew up with carbs (my other car is a Mustang II) so I have a love / hate relationship with them (easy to bolt on yes, easy to tune not so much, easy to start in a Cleveland winter heck no). But you have your preferences so those are obviously the most important to what you do with your / your daughter's car.
I think your long-term goals are most important. An AODE isn't the strongest transmission by far, though it can be built up quite a bit, and a manual valve body would fit for street / strip use if you don't mind the extra motions (a nice shifter would probably help). If it were me, and I had plans to make it a 9 second car, I'd go with a built C4.
But to be honest none of this is speaking from experience, both of my Mustangs are manuals, so there's got to be better opinions out there. The SN95 section of this site is pretty small, you might try posting the question in the general / Fox forum.