1. Starting faction settlements are defined in descr_strat. You would have to move every single settlement of every single faction besides the capitals to the Rebel faction section in descr_strat. You also have to remove every faction's armies and generals which are located at those settlement's coordinates.
2. I'm actually doing a 12 TPY campaign right now. There's only two things you have to do. First, change your timescale in descr_strat to 0.084. Second, insert an aging script into your campaign_script file. I'll give you the one that I'm using.