For fluency, I start off by modeling how language should sound based on the author's purpose, intonation of the text, and punctuation. I even allow my kiddos to do the read aloud so that they learn that it is a shared experience between teacher and student. I often do mini running records in between the assessment periods so that I can keep a better pulse of who is growing or not. Putting kids in small groups of heterogeneous members also assists all readers with fluency.
For comprehension I do the following:
-small group work throughout the year
-interactive learning with small and large based projects or group work (e.g. poster displays, games they create, PowerPoint presentations, or other multimedia outcomes like Prezi or Popplet) to show understanding of the text we read
-exit slips with 1-2 questions
-reading quizzes
-many, many mini lessons on comprehension strategies such as Turn and Talk, Think/Pair/Share, Cubes, Create the Story or Model/Act Out the Story using words or pictures, and Graphic organizers based off my model or kids create their own including anchor charts on what they learned
Hope this helps!