A Major Issue I've not seen mentioned
As Japan had its arable land nerfed with the update, it now only barely has enough subsistence agriculture for the starting population.
So as the population grows, every new person born becomes unemployed rather than a peasant and becomes a radical, causing almost every (if not every) state to enter a constantly worsening state of turmoil.
This only stops worsening once your construction sector can only keep up with and overtake population growth after getting steel-frame construction and a large investment pool probably around the 90s
The issue is genuinely unsolvable without it: Lowering taxes reduces radicals but even further weakens your already too weak construction sector (or causes you to enter an even worse debt spiral). Raising taxes and maximising construction causes your radicals to spike and leaves you quite literally unable to form a functional government (after ending Bakufu). Deficit spending also doesn't let you catch up and only puts you in a very precarious scenario.
The only real way to counter it is through funding the police as much as possible, but that only reduces the effects from the radicals and doesn't solve the crisis.
The game needs a fundamental rework of how peasantry and unemployment works, but as that's not happening any time soon I think the easiest solution is to simply add more arable land to Japan, so that new pops become peasants rather than unemployed; even if it's inaccurate to their actual arable land.