Definitely don't take the stockers off unless you have a specific need/desire for some specific behavior that that would cause.
What behavior are you wanting to alter in the first place? Too much oversteer, too much understeer, or too much body roll in general?
If you don't replace them both at the same time, you run the risk of inducing too much over or understeer depending on which you do. Just remember, stiffer rear will reduce understeer (too much and the rear will be very loose), stiffer front will reduce oversteer (too much will cause very strong understeer).
Edit:
If the answer is "too much body roll" and you are otherwise happy with the handling balance of the car, you definitely want to make sure you replace BOTH anti-roll bars at the same time with a nicely matched set. That way you will keep your balance.
What are you trying to accomplish? I am assuming you are trying to remedy the understeer issue. I too have a GT ragtop and I noticed it had understeer issues with the stock suspension. Since you are on a tight budget another option would be to get an adjustable sway bar for the rear. I know a few companies sell these and from what I've read they seem to work. That way you can stiffen the rear a little (which is what it needs) and get a more balanced car for cornering. Some of these adjustable sway bars allow you to keep the stock sway bar in place. The front sway bar on most GT convertibles is around 30 mm which is fairly stiff but the springs are softer than the hardtop GT's. If you are serious about handling you should look into installing, in the near future, SFC's, stiffer springs and better shocks (which is what I did). The nice thing is you can later "tune" your sway bars with the adjustable rear swaybar after you do more suspension mods.
According to MM, the stock front sway bar is > ALL.. that is why they dont make one for the 96 and up stangs...i had an hour of suspension chat with them a week ago... your choice though..
To me, suspension upgrades would be all the rear control arms and decent quad and rear shocks. The GT suspension is probaly as stiff as you would want. For example you can jack one side of the car up and lift the entire rear end, provided that you use a decent control arm. W/control arms alone your car should hug the road like it owns every bit the pavement. Besides there is not much difference between the stock and aftermarket sway. Ours I think is 26 MM. I would suggest some ball joints new inner and outer tie rods and bushings for the sway bars you have. My car felt brand new after those were replaced.