Puzzle answer for Shiro's warehouse (not super difficult) is Left, Up, Up, Right, Up
There isn't really much help with the sneak sections, just call Mako for help to distract when you can and git gud.
The four optional ladies post game are the helper at the brothel (deliver a message to Shiro at her warehouse, then come back), a new junior in the Red guild (in basement, then commercial district, then back to basement), the washing girl at the Justice guild (buy soda?/soap? from top left shop pick the lady, then go back to Justice guild), and the Azumi deputy captain (drinking in bar, head back to kitchen at Red guild to get booze, go back to bar, then upstairs).