Well, there are a few things I consider requirements for a Mustang. Frankly most of us stang owners do much more cruising than we do racing so get the appearance and sound right first IMO.
1. Exhaust. There are tons of combinations you could go with so I'd listen to some sound clips on you-tube to decide what you want. Depending on your state's regulations you may need to have cat's to pass emissions. I really like the fit, finish, and sound of my Magnaflow catted x-pipe (they're spendy, but worth it IMO). Catback isn't really necessary and won't net much (if any) noticeable HP gains on a stock Mustang. If you're on a budget there's nothing wrong with buying a pair of mufflers you like and having them welded in place of the stockers. I bought a MAC cat back and while it sounds mean as f**k the drone drives me crazy on long highway trips... something to consider. On the other hand, if you're of the mindset do it right the first time, may as well buy a cat back you like.
2. Suspension. These cars are notorious for having a high ride height from the factory. I'd get some lowering springs and new shocks/struts to start with and you'll be amazed at the difference in handling ability. I love my prokit springs. The ride/handling balance is good and I was quite pleased with the drop (I didn't use iso's in front). I think H&R SS springs provide an awesome very aggressive stance, but I couldn't have them in MN with these chitty busted up roads cause it would drive me nuts. Depending on what springs you go with you may need CC plates to get the alignment done correctly. Then get yourself some full length subframe connectors and take them to a good shop that can weld them in on an exhaust lift that lifts the car from the wheels.
Beyond that it's really up to what your future plans are with your car. My car is a sunny day toy and I wanted something that sounds aggressive, handles reasonably well, and most of all looks sweet. I've chosen my mods based on those goals. I've never been to a 1/4 mile track, and with my cams the car has a sick idle, a fairly flat torque curve, and emits sweet music out of the tail pipes when I get on it. I love the way it looks w/ my lowering springs and wheels, and it's really fun to drive on windy back roads.
Hope that helps. Give me an idea of what YOU want out of your car and that will probably help you decide whether to do some simple mods like PI intake and cams, or save up for something bigger like FI.
EDIT: BTW the Lincoln Mark VIII engine you'd want was produced between 1993-98