Well if you love the car you would drop a V8 in it like the 2010 boss V8. its a 6.2 liter engine, It will give you about 500 horse power. I also recommend buying Performance chips for the engine, they can add extra horsepower for speed and acceleration. Also recommend twin turbo chargers, replacing the transmission with manual because once you get good with a stick it will increase your speed by a few mph. You can also change the gear ratio (higher gear ratio for higher speed, lower gear ratio for faster acceleration) Also you can replace the camshafts, mash the induction system, replace the exhaust system that lets it breath more freely, and that should be about it.
The highest performance gains always come from turbochargers. Sadly that V6 mustang has far too high a compression ratio to try to turbo charge it. However, a small supercharger would be reasonable and could easily give you 40-60 more horsepower, but installation won't be that cheap. However, it will be much cheaper in a dollars/horsepower than a cold air intake.
you are on the right track,tune up is the first thing,cold air is good,but for the air coming in to be as helpful as possible,adding flowmasters in place of the origanal muffler along with new pipes and then the good air coming in will not face back presser on the way out.i always do both as they complement each other and you should pick a few hps and a few mpgs,and it will sound cool.good luck.
Not much you can do there, friend, unless you plan to spend big money. You can try and make your car lighter (remove spare tire, tools, even the back seat).
You might also look for a high-flow exhaust. I'm not a huge Mustang guy, but there may also be an ECU program/flash for your car, so look into that. There are countless forums and websites dedicated to Mustangs, and those guys should be able to point you right. Good luck!