Thanks for your help. Will need to troll the forums as well. The beginners guide doesn't really go far enough for what I want to do.
Nope, but it does show you the ropes of how mods come together

I went to the download page and I can only see forge and particle engine. No tools that you mentioned.
The tools is a rather generic term.. there's no GUI editor for entities or a generic "modding" program. Notepad is your friend. The archive for the Forge Tools download (below Particle Forge) will contain a Reference Data folder that contains text versions of every file the game uses. This isn't just GameInfo, it's also files from Window, etc. Everything you need is in there.
Regarding fleets and techs. I wasn't so much after what a player could do potentially but what each race starts with. For example I want the Vasari to start with a fleet and the tech that allows inter solar system travel. Are they all in the same file (PlayerPhase entity file) or do I use templates for that?
You can't set researched techs at game start, unfortunately. The starting units/buildings for the various races are defined in galaxyScenarioDef.galaxyScenarioDef and are held in the homeworld templates. The galaxyScenarioDef file is a little confusing, but not too difficult to figure out if you look at the templates and do in-file searches for the names it uses to see where they come from.
Also, how does the game know if the map is small, large etc? Is that something you set or something it calculates?
I believe you set the "map type" (2v2, 4v4, etc) when you create the map, and that's how it knows if it's small/medium/large.
And is it possible to create phaselines between stars using a text editor?
Stars are all automatically connected, you don't need to create anything