Again, this depends on your style of game. You can run straight to it or throw missions in between or you place the missions and wait for the players to stumble over them.
Think of it like a serialised show like Picard or metaplots in TNG. I, personally, prefer alternating of some sorts and this works with my group.
If in doubt, ask your players what they prefer and talk to it within your group.
Does anyone know if there are, like, enemy cards? Even blank ones that you can fill in? Flicking through various PDFs to get to stats feels like it might be awkward.
Also with balancing starship combat, the CRB only mentions the number of players, but doesn’t seem to offer advice with respect to the ship they’re using. Intuitively, you’d expect 5 players on a Sovereign to do significantly better than 5 players on a Nova. Does that bear out? How do you account for the class if it does?
Actually, there’s one on p. 13 of Shackleton. 
The Replicator Resources section of the Continuing Missions blog might have something. If not, I’m afraid you have to resort to the word processor of your choice. 
You’re referring to p. 301/302 of the CRB, right? The rules more or less assume that your group uses a Scale 4-5 ship. Number of players and enemy scale is far more important than player ship’s scale, as number of players and enemy scale equal turns. Lager ships have more resistance and a few more points than smaller ships but it shouldn’t be too much a factor. I’d say: No need to modify the advice on p. 302 if players are using a Scale 4-5 ship. Put less pressure on them when they fly a scale 3; more, if they have a scale 6.
Thanks for the link! I don’t think there is (I didn’t scour the whole thing, but I checked a fair bit and didn’t see anything), but it’s an awesome resource!
Yeah, that’s the one. Looking at the guide then…would you say a rule of thumb is that enemies equal players when they have, cumulatively, 1.5x the player scale when their security <3, but if their security is > or = 3, then it drops to about 1x?