First off, welcome to the site, sounds like you are semi-knowledgeable.
For my first point, do not ever, I mean ever, order anything from rpm outlet. They are notorious for ripping ppl off.
ABS and TC are both options, my 02 V6 had neither, didn't have cruise control either.
Since both door locks are not working, are you sure it's the actuators and not just a blown fuse or faulty wiring?
The speakers sizes are 5x7/6x8's, both will fit with no modification. As far as subs, that's up to you and what your budget is. I fit 2 12's in the trunk with plenty of room to spare...
On the headlights, you will either have to sit down with sanding paper (starting around 1000 grit and moving finer) and really work on wetsanding them down or just buy a new set of headlights. If you buy new, the smoked lights look great.
The hood scoop is bolted through the hood, remove the inner liner and take the bolts out and it comes off. The sidescoops are simply pressed on, you can pull these straight off with a little force and do whatever you need.
Do not buy the gullwing door hinges, these are notorious for rusting and having alignment issues. You will fight them from day 1.
You're getting about the right gas mileage for right now, if you are just wanting to make the car a little more enjoyable I'd recommend exhaust, cai (if you want), and a good tune. The tune will make the biggest seat in your pants improvement while also being able to bump up the mileage a little more. The exhaust will just be more enjoyable overall.
For more information on modifications I'll point you to this thread:
It's a list of modifications put together by some of the forerunners in V6 performance and modification on these mustangs.