Shortly after this, Minamoto annexed the everyone.
Honestly, the best I could do. It's so dependant on luck. The change of truce times makes Japan much more placid and hence there are less places that can be used for patriot rebels. I noted that you can use anywhere that is rebel occupied as a base for patriots, so Ikki-Ikki occupation can be exploited a fair bit (speaking of which the localisation for the Ikki-Ikki rebels still hasn't been fixed).
Asia is really, really limited in terms of what you can do, the comparitive glut of decisions for Christians and Europeans is so overwhelming. If it weren't for the AI's stupidity I'd be absolutely behind in terms of income.
I could try again and optimise a little (I lost at least 100 years on noble rebels resetting the slider for plutocracy - which is the most important slider to you in this game, aside from perhaps centralisation for spy efficiency).
Settings:
Advisors: Historical (This is bugged because if you create an advisor, and they lack a death-date, they are immortal).
Merchants/Spies/Colonists: Normal
Difficulty: Very Hard
Aggressiveness: Low
Map Spread: 200 Years
Lucky Nations: Historical