Just got a 1999 GT 35th

CONGRATS ON THE PURCHASE! And welcome to the forums .

Ifs its a 5 spd, then get an aftermarket shifter (MGW would probably be the simplest way to go and give a great shifter right out of the box).

Next would be a handheld tuner from SCT (Xcal2)

Then maybe some 3.73 or 4.10 gears

Those would really help the car, and would be more driveable than stock...you would like you car much better.

Short throw shifters are nice, but if you like the stocker I would hold off on an aftermarket shifter for now. If you dont like the stocker, try and find a Mustang with a short throw and see if you like the short throw. MGW is the best there is, but they are expensive for just decreasing shifter travel and automatically finding 3rd gear.

Id get a midpipe first, then a catback so you can get the sound department taken care of.