Kuroda Sisters

Kuroda Rico (1st year) and Kuroda Miko (3rd year) can be found and completed in the Kagane Route.

Rico:
Stage 1-2: Behind a pole at the school gate.
Stage 2-1: Walking at the end of the empty hallway.
Stage 2-2: Ducking behind a shelf in the back of the cafeteria, behind the counter.
Stage 4-2: Hiding behind a pillar under the stairway, poking out her head shortly.

Miko:
Stage 1-1: Across the bridge, directly ahead in the center of the screen, if you eliminate the first 2 girl of the level in time.
Stage 3-3: Hiding in the top left corner of the room, in a room you will only see if you don't shoot anyone during the section of the level you are hiding under a bench.
Stage 5-2: Running away, if you eliminate the student and teacher that run past, at the end of the hall before they reach the other hall that they would run down. (Done by using a Doki Doki Mode.)

Kurado Mako (2nd year) can be completed in the Kaoruko Route.
Stage 2-4 (x2): She will briefly appear at the center of the screen once you finish scaling up a pipe. She'll appear again after going down a floor when you peak through a window. She'll be sitting on a bench to the left, facing away.
Stage 5-1: Towards the end of the level, four girls will appear at once as you scroll by. She is the second from the left-most girl.