
Question 1: BW's right. I can't remember the last time I used and-in-sequence. Using 'and' in your case is perfectly workable.
Question 2: Is this supposed to appear at the start of the mission? If this is the case, then you don't need a dummy event. Just set the directive on its own, and it will show up at the beginning of the mission. Only use chained events for directives that have to appear after a certain message or event (i.e. shortly after 'X' jumps in, Command orders you to take out its beam cannons; after Command gives the order, the directive pops up from a chained event).
Black Wolf is right here, but I just gave a simpler suggestion.

Question 3: What Black Wolf said. Having a ship appear without a warp effect does the same job as having invisible to radar, except that the ship isn't in the area until it is detected. If you're looking for a ship to simply disappear, use "ship-vanish".