The first thing I would suggest is to check how much insurance is going to cost you as a 16 year old with a RWD V8, this might make the car too expensive to own. As a whole the 4.6 is a stout engine and in the 10 years that I have owned my stang I have had no major reliability issues, hell I am just this week replacing the stock battery.
Now, honestly, for me at 16, it would have been a death trap. I was and am a responsible driver, but I still sped more and did crazy things in my first car (a mercury sable) than I ever did in my mustang. This was a combination of teenage invincibility and lack of experience / not really understanding consequences as a driver. But this is a case by case thing, I know some 16 year olds that having a mustang for their first car would be no different than so slow tank of a car.
The 99-04 has a few Naturally aspirated mods, meaning no super or turbo charger, that are "easily" bolted on:
Rear gears
longtubes and mid pipe
Plenum and Throttle Body
and basic
suspension upgrades.
The stock engine is only going to handle around 400rwhp before you are in danger of blowing it up. And you are going to need all the basic bolt ons plus cams to hit 300rwhp w/o forced induction.
to address some of your other points/wants
The CAI is worthless HP wise and basically a cosmetic mod.
Also, I don't know if LED brake lights and sequentials would work. Personally I think anything other than stock or tinted headlights/taillights look cheap.
Wiring the mustang for a sound system is not too bad and can be done in a day, if not done as an entire set, do this: Replace the stock speakers with a decent set of components, then the head unit and a 4 or 5 channel amp and then subs. I did head unit and subs first and quickly destroyed the stock speakers and had to driver around with good bass but garbage everything else until i could afford to fix that.
if you get a 2000-2004 mustang it will come with a hood scoop
Look around read a bunch of threads and learn about the basics.
Though, to be honest, if I was going to get a mustang when I was in school, I would have gotten a Fox body and built a 2.3t and saved a huge amount of money insurance wise.
Also, on a side note, while I daily drove mine for years in PA winters, I wouldn't recommend this car as a first car if you will experience snow.