For the speaker wires you'll need to follow most of this:
1994-2004 Mustang Door Panel Removal
As well as this:
2001-2004 Mustang Aftermarket CD Player Installation
in order to access most of the areas.
For installing the 4 gauge wire, run the wire along the driver side, there is a grommet that is fairly easy to get to, pull it out or slice it and run the wire in that way. Remove the kick panel and the bottom trim so you can pull the carpet back, run the wire along there, you can then push it behind the rear panels. Now, pull out your rear seat (if you have questions on this just ask) and you can run the wire into the trunk this way, leaving it under the trunk mat.
As far as running the wires, it's a fairly involved process, one thing to remember is avoid running any rca or speaker wires alongside the power wire as this will give you unwanted feedback from the speakers.
Are you wanting to run an amped setup or simply run everything off the cd player?
I've done all this before, so any detailed questions just let me know, I"ll search my archives of pictures when I get home tonight and see what I can find from you.