Going around the ship clockwise or counter clockwise is about the same. Breaking the skylights from below on the right side of the ship can be done with carefully tossed breach charges as well.

Ending in the center of the ship saves the most time because it's a long walk from the dark room with the heavy door.

Tiny Trouble (the one that run away) must either be killed or arrested. Killing them subtracts points from your score. Arresting them adds points, but is obviously slower then the alternative.