I need to know how you:
1) Have ships enter hyperspace
2) limit availible craft

For part one I have a flight group (with player) that I need to have go from region 1 to region 2, then to region 3. Currently only the player craft will do this.

For part two, I have a the player in an x-wing flight group, and he can currently switch to whichever rebel craft he wants. How do I limit the availible craft to just the X-wing?

1/ You've got to set up the order for the flight group to "hyper to region #", Region 2 (can be done easily with AlliED). Set the first waypoint for this order near the hyperbuoy, otherwise the crafts wil enter hyperspace immediately.
2/ You've got these options available in AlliED. NB: when you launch missions from the flight simulator, it does propose all Rebel ships, whatever you have set up (so I think).

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Fleet Admiral Striker, Emperor's Hammer Strike Fleet
http://www.emperorshammer.org/)