wakethis2006

I have a 1996 mustang GT and it has a cold air intake. I am getting ready to put some money into it and build it but not really sure what i should do to it. Could i please get some good suggestions on what to do to build up the motor for to have a good amount of horsepower and torque. Please let me know some good things to do.

JC316

PI Head Swap
Long Tube Headers
Gears
Nitrous

Lowtryx

You need to look into the PI Swap. Not only does it give you the better baseline for power applications, many more mods will then apply to your vehicle. Not much applies to the SN95's when compared to the 99-04 models.
First and Foremost, PI Swap. Gears, Full exhaust (Headers, X Pipe and Catback) Underdrives and Dyno Tune.

A handheld tuner won't give you quite the power you would want to offset the cost, it would be a much better idea (more bang for your buck) to just get it Dyno Tuned after the PI Swap and exhaust.