After many years of modding TLD I couldn't touch M&B or mods for a while (a few years).

But when I did again, I got into Gekokujo and am loving it. Really great effort!
Bug:
Got 3.0 off ModDB, so I noticed 3.1 is out a bit late, so not sure if this issue is fixed as part of the "disappearing companions" mentioned in the changelog or not.
But the issue I've noticed was, I took a fort, claimed it, installed a minister, then when I wanted to replace him with another companion, the new companion became minister, however the old minister didn't become a companion again, but went missing. His notes entry says "wherebouts unknown" and he's nowhere to be found.
But apart from this, I didn't notice any gamebreaking bugs. Well done!
Suggestion:
Ever thought of using the tableau system like the vanilla game uses it for heraldic armours, to enhance your existing armour models to have faction-specific variability? Like, the base colour of the any lord's flag could colour some select bits of his troops armour, like the undershirt or the ornaments on armour? You could even already attach the nobori flag to the armours this way. This could give each lord's troops a very unique look, without having to actually make all the colour varieties of armour, but use only one model type each time.
Cheers!