As far as mods go you'll get all kinds of opinions.
But almost everyone agrees that gears are one of the cheapest, higest impact mods you can do. 3.73 is the magic gear for the 5.0 Fox Mustang. This one part will radically change the feel of the car.
After that, you can do what you want pretty much.
I'd recommend a shifter, any shifter. They are all better than stock. Find one that fits your budget and buy it.
Looking back if I had it to do all over again, I would go for head and an intake first. Then the little stuff to support it.
Enjoy the car. It'll be a fun ride.
Common problem areas for rust are the bottoms of the doors, and the underside of the trunklid/hatch. Some cars have leaky rear main seals, while others look like they have leaky rear main seals and actually have sucked the rear intake to block gasket in and oil is leaking out the back a little bit. It's common, not a very big deal. With the age of the Fox body cars you gotta start looking at just general wear and tear. They made tons of these cars so look for the nicest one you can find.
If you live in a hot dry location, look at the condition of the suspension rubber and the interior fabric. If it's a convertible take a close, hard look at the top material. New top installed is about $800-$1000 at an upholstry shop.