Engine Breathing
The decision is simply one of economics. For proper upgrading all parts of the breathing system need changed, intake, heads, exhaust.
I just finished swaping/upgrading my 95 GT w/ Ford racing parts, aluminum heads, 1.7 roller rockers, GT-40 intake, 65mm throttle body, headers and exhaust. I did the suspension at the sametime and a huge difference. Set me back about $3000 total.
If $$ are tight start with the easy stuff, Intake, Throttle body, free flowing air cleaner and then move on with the rest as $$ permits. If money is real tight lok into the explorer intake. Not as good as the GT-40 but can be had at the junk yard.
PS, I used the 1.7 rollers because they give you about the same performance increase as a mild cam without having to tear apart the engine. Also, you can get the GT-40 iron heads a whole lot cheaper if you are not looking for the weight reduction.