Not much to add to the clue book. The game flies well without much in the way of suggestions or problems.
On the mission where you track the last pirate instead of kill him -- stay a good distance away 20-30k is fine. As soon as "mission objective accomplished" -- head on home.
You can use leech missiles to stop some cap ships instead of torpedoes.
Also, on the "destroy the Lexington" mission, use [C] for com, chose one wingman, then the other. First, lock on one cluster of enemy and issue the command [C, then attack my target]. Then, lock on the other cluster, use C and tell the other wingman to attack my target. This will tie up all of the enemy ships.
You can then barrage torpedoes, from a safe distance out (torpedoes don't get shot down when launched from a distance) or you can barrage leech missiles.
The above are major changes from WC3 where Leech missiles were useless and torpedos got shot down if not fired from close up.