Looking to add a bit more hp....

Underdrive pulley set will help, long tube headers, and the proper cams with a dyno tune will get you over 400 crank HP easy

id get your heads ported, a set of cams, longtubes, and an intake.. that should get you well over 400 crank hp.

Porting the head for 400 crank HP is not needed, if you're looking at 400 at the wheels then a set of "big valve" FRPP CNC heads or Livernoise heads with the proper cams will be required.

Dudes, the whole point of his question is that he doesn't have blower-level money. Cams, ported heads, a full LT exhaust? That's the $5k right there that he says he doesn't have.

To the OP:
1) jump to a 93 octane tune, there's a bit more the be had.
2) Ford Racing intake plenum and throttle body (roughly $800 if you do your own labor). will go well with your CAI, and opens up the top end a bunch. Plays really nice with better cams or heads should you go that route when you do have that kind of cash to play with.
3) GEARS! It will make your car feel a lot more powerful, shouldn't cost more than $400 at a local shop, and it doesn't involve messing with your motor. If you are running factory cogs and you jump up to a 3.73 or a 4.10, you will definitely notice the car pulling a ton stronger.
4) high-flow midpipe and a catback. This can make your car sound better, you can do it piece by piece because if it's all stock style it all works together (IE- midpipe now, catback after that), and it will help you pick up some oomph. LTs really won't be worth the hassle unless you go crazy on the motor or put a blower on it, and with LTs you have no choice but to at least do headers and a midpipe in one shot.
5) full suspension kit. yeah, I know it's not horsepower, but if you can put down and keep down all the power you have now, your car will feel faster. Roughly $1200 for a complete kit from a company like Roush, and being able to lay down up to a 1G lateral turn will really allow you to carry the power through turns around town.
6) better tires/rims. Again, better handling allows you to maintain your pace and keep more power planted. It can either compensate for your stock suspension, or complement an aftermarket one by really holding the pavement. Less wheel hop=better acceleration. Better grip=more speed with lateral G loads (on/off ramps etc.)

You aren't going to see 400HP to the wheels without getting into the previously suggested heads/cams/intake/long tube setup or some kind of forced induction on a 4.6L motor. That's 5.0 Coyote power, and without some serious modding to a 4.6 to level off all of the advancements, it's just not reasonable to expect that kind of output from the 3V. Sometimes beefing up the stuff around a motor can make the car feel like it has more power because you are able to efficiently harness all of what you have. Good luck, and keep in mind that once you hit that 400HP mark, 500 is going to be waiting there, daring you to chase it down.

CAI, tune, headers, gogo

someone probably put a muffler delete on it

If the car is lowered, it could just be springs. The rims and tires are a nice start. If there aren't mods to the shocks, struts, sway bars and other supporting suspension pieces you could eye that to finish that area of improvement. I agree that it sounds like somebody just hacked your mufflers off. You can leave it, change to a catback that you like, or splice in mufflers you like. I spliced Magnapacks into my factory pipes because they are more than big enough to handle what I am putting through them. On the red brake shoes- could be anything from spraypaint to Ebay pads to top brand pads. If they stop good, then wear them out and get new ones when the time comes. If the braking sucks, junk them and get something better.

Hate to be technical, but they're calipers and rotors on a disc brake setup, not shoes as would be on a drum setup.

Minimal. Any and all you mentioned are about even in gains over the stock choke-boxes. There isn't a ton to be gained in the muffler department anyway until you really start pushing high numbers, but it does allow you to tune the sound of your car, and IMO the sound of a Mustang is as important as anything on it.

Maybe some weight loss can help... Drive shaft? lighter wheels, rear seat etc....

I looked real hard at doing this, but what it finally came down to is like 65% of the performance for 75% of the cost. Unless you have some total desire to stay NA, it is more cost effective to go FI.

Start simple: exhaust and intake. But you will need to figure out what's already been done.