I just replaced every speaker in the stock locations in my 91 hatchback. If you want a undisputed answer go to crutchfield.com and use there "What fits my car" application.
I used 3.5" in the dash (79-93 same size), 5.25" in the doors (I know that the 87-93 use this as stock), and 6"x8" in the rear (79-93 same size).
Now these are the stock sizes, but you have to be sure that the speaker you have will work with the stock mounts. Take for instant, my door speakers needed to have the mounting holes redrilled. 6.5" speakers will fit in the doors with a 1/2" spacer for most brands/depths.
If you are going to be placing speakers in the doors, I would sujest you look into components and put the tweeters in the dash.
Proud Mustang Owner since 1994
1990 LX 5.0 - 3G Alt. Upgrade. More to come later!