I just put in my aftermarket stereo in my 2000 GT last week, and I was a complete beginner to this whole sort of thing. It is incredibly hard to find actual professional videos and info on this matter, so you will be doing a lot on your own. I'll try to help you with what I can. Beware, there's a lot of text.
Because our years shared the same style of radio, I am going to assume you have one single DIN stereo deck/cassette player and one single DIN CD player. Hopefully you understand what I mean by DIN.
You need to pick up a set of Ford stereo removal tools. Scosche DT1 - DIN Radio Removal Tool: Auto Electronics : Walmart.com
This video will help show you how to remove the factory stereo. https://www.youtube.com/watch?v=8-eW0CIJW0c
2000 Mustang GT
My pride and joy, my first car ever. Bought on 6/2/2013.
Check it out at my channel here: youtube.com/mustangfanatic95
Expect more vids in the Spring: Car shows, cruises, fly-bys, etc.