Factions: You can run as many as you like. I've run games with
every available mod faction before. You need to increase the RAM allocated for Starsector to do so, though. You can find the settings in your Starsector folder, by editing the "vmparams" file with, say, Notepad, and giving it up to, but
not more than 8GB of RAM. Java cannot handle more than 8GB all that well.
Look for:
windows -Xms1024m -Xmx1024m -Xss1024k -classpath
For 7GB, change it to:
windows -Xms7168m -Xmx7168m -Xss1024k -classpath
Battle Carriers: Hresvelgr (Red Guard & Legio Infernalis variant especially), the Scalartech Filament, and several new Legion variants come to mind. Also, Kadur Seraph, and the Midline Triumph. There's a lot waiting for you.
Mod Installation: Download the mod from its respective source, then unpack the file in
[...]\Fractal Softworks\Starsector\mods\ - that's it.