FRED actually comes with a tutorial that covers making a full-fledged mission from scratch. Go to the "Help" menu, click "Help Topics" and then select "Walkthrough" to get started on it. If for some reason you don't have the FRED help files, there's a link to an online version of that same tutorial in the FRED section of the wiki.
If that's not enough, there's a few useful articles on mission design over on the old Volition Watch site, to which this link will take you:
VW Articles Page. Scroll down to the Freespace section and look for anything regarding FRED or mission design.
Finally,
Karajorma's FAQ has a very helpful section on FRED; in particular, check out the "Common Mistakes" section to see some of the pitfalls that you want to avoid. Not exactly a tutorial, but avoiding those mistakes is nonetheless a good thing.
As for Shivan fighters, yes, this is possible. It requires altering the ships.tbl (or using a modular table to modify it) table by adding a "player_ship" flag to the entry of the ship you want to fly, and then making it available in a mission. However, if you're going to be messing with the tables,
definitely back up the one you're working on before you change anything - You can very easily break something, and if nothing else you will need the stock tables for multiplayer.
