Sorry, I wrote that from my bed while still half asleep.
If you have already got cores on all or most of Japan then it is absolutely not worth it to unify Japan. The benefits of being Strong Shogun would be stripped away and all you should get is +50% naval forcelimit and a cored Kyoto. If you embargo Japan you could probably force Kyoto's CoT to stagnate to death (your goods would provide no value to its CoT) and build your own one. +30% tax is a hell of a lot and the lack of ships you can overcome by just building light ships for tarrifs, which are cheaper, or with the National Idea and high level naval buildings.
I've also heard reports that if you gain infamy through wars with foreign powers, that infamy goes to Japan rather than yourself.