Light red: there is a nub on the bracket that must be placed in the circled hold.
Dark red: this is the pressure regulator valve plate that is removed after the lower valve body is removed.
Green: pay attention to the routing of the wire and how it is in the circled clip
Purple: the arrow points to the dowel that aligns the lower valve body. The dark purple visualizes it.
Blue: the arrow points to the groove in which the shift linkage must be aligned into during assembly.