Nice to hear that you and your dad are getting involved in this project. I still have my 97 GT and the first thing is a good intake, followed by exhaust. The order is up to you, but try to do one intake, one exhaust, one intake, one exhaust, etc, so you have just as much effect going in as you do coming out.
Exhaust wise, if this is your daily driver, get a catted x-pipe (only if you have emissions inspection in your state). You'll get much less restriction and more power, but still stay legal so you don't have to keep switching it out (which becomes a pain). For the catback, it's all up to you, but I personally like the Pypes Catback. It's got a good tone and a noise that no other brand has.
In terms of intake, get a CAI, bigger throttle body and plenum, and an intake spacer, along with better ignition wires and spark plugs. If you really want to, do a PI swap, but otherwise that's about it for terms of power. Hope this helps!!
2014 Ford Focus ST (ST3, Tuxedo Black Metallic)
1997 Ford Mustang GT (Rio Red) (RMR #7832)
2003 Ford Mustang GT Centennial Edition (Black) (SOLD)
2004 Ford Mustang GT (Redfire) (SOLD)
1985 Chevrolet C10 Custom Deluxe (Red) (SOLD)