At this link: https://www.thedailycafe.com/cafe/assessing-student-learning/assessing-each-strategy, there are assessments for most of the strategies on the CAFE menu. I might suggest looking at the rubric at the end of each one, and use what you’ve observed about your students to rate them. If you have a question as to whether the student has that strategy under his/her belt, there is a lesson about how to assess it.
If 80% of your class has that strategy under control, you don’t need to do whole group lessons on that, but rather have your student conferences center around those with specific needs. That will begin to narrow the focus. Make sense?

The “Sisters” suggest 6-5-4-3. So starting from left of menu, Comprehension, the first six strategies under that heading are the most important. Then the first 5 in Accuracy and so on. Does that make sense?

The beauty of the CAFE concept is that these strategies are a continuum of good habits. My interpretation is more of an ongoing use rather than reaching mastery. When reading materials become more challenging we refer back to the board and use those strategies when necessary to read those challenging texts. I find myself using the strategies even as an educated adult when I am reading text that is complex as well. So I guess my answer to your question is not to worry about those who appear to have mastered some of the strategies. They will still need to pull from that knowledge as their reading levels grow.