A. Ancient Israelite and early Jewish materials
It makes sense to read the Ancient Israelite and early Jewish materials in chronological order. Beginning with the Introduction to each text (uploaded separately), and then the text itself:
The Biblical passages
The passages from the Temple Scroll
The passages from the Mishna (tractate Yoma and Chapter 5 from tractate Zebahim)
Keep in mind that the authors of the Temple Scroll and of the Mishna had both read the Biblical texts you are preparing (in pretty much the same form), but there is no reason to believe that the authors of the Mishna would have read the Temple Scroll.
As you read the passages from the Temple Scroll and Mishna tractate Yoma, ask yourselves how the two differ in their understanding of Leviticus 16.