Since I posted each route separately, I might as well make an index post that links to the walkthrough of each route. I just followed the walkthrough on otome.girly.jp and translated the choices to the localized version.
There are a total of 6 routes. You can play them in any order, but I’d suggest Hijikata’s route for last because it is the longest and sticks with the Shinsengumi ’til the end. It’s pretty much the “true” route.