1. How do you actually join a faction and fight for them?
Hmm. I may have to change the text description here a bit, to make it clear how play works.
You don't join a Faction. At the start of play, you pick your "former employer", which sets your relationships with various Factions to the same as your former employer's and gives you access to certain ships. Think of your former employers as your "allies".
However, your
overall goal is to take over the Sector; to do that, you'll need to
start up your own Faction and completely defeat your enemies (whereupon you get a victory screen). That is, and will remain, one of the core goals of the mod.
This you can do by building Stations (land on a planet to learn more about that), which can then build fleets, which can destroy other Stations and build new Stations occasionally on their own. It will irk all of the Factions in that System, though; they don't like it when you encroach on their territories. So be careful
2. Is there a journal anywhere which keeps track of which systems have which factions and what stations a faction controls? And that also keeps track of all the alliances and enemies a faction has?
Not yet. The faction relationships are static, in terms of who's allied with whom and all that; they don't change over time atm.
This may change later, if I want the AI factions to gang up on whoever's the most powerful or whatnot, but it's currently static; your character has emerged into a specific historical scenario, so to speak, and the wars that are on-going have been going on since before the start of play.
In terms of displaying that data, the main issue is that we can't see anything in Hyperspace that shows where enemy / friendly bases are, so it requires some exploration to figure this out, and can take quite a while, if you choose a really big Sector size.
Anyhow, I think that can be done with some OpenGL but I've been pretty busy working on other things and haven't taken a serious look at it yet.
3. Is there a repository of all the ships of a faction?
No; the Codex doesn't allow for sorting by Faction, and the huge number of ships in the mod, and the relatively frequency of change makes building some static Thing here on the Forums pretty un-attractive.
Perhaps there's a way I could do it within a Dialog automatically, though, so that players could view that data at Stations instead. I will definitely look at that, it's a good feature idea for newbies