Sounds like you are well on your way. Don't forget a can of brake parts cleaner. You'll need that after getting everything in place to clean off all fingerprints, etc.
I did my first clutch job when installing my new Tremec 3550 this summer. It was easier than I thought.
Make sure that when you tighten down the pressure plate bolts to do them in a crossing pattern over several times. Definately use a torque wrentch in order to attain the proper ft/lbs. The clutch alingment tool is a must as well. I replaced my rear main seal when I was in there too. I am not sure about whether yours is a 2 piece or not. You may want to consult a Chiltons manual or call your local Ford dealer.
I didn't replace my throw-put bearing since I only have 39,000 miles on my Stang - plus I've heard that they are a pain in the rear to take out.
Good luck and let us know how it goes or if you have any other questions.
E