There’s a lot of good advice in this thread, but hopefully I can at least help with this part. Tobira wasn’t originally designed to be a self-study book so there is some vital “how to use” information missing imo.
I’ve taken some language courses like you have, and the way my instructors taught us to use the Tobira textbook was to treat the reading passage(s) as the essential central piece of the chapter. It’s not meant to be read in one fell swoop, like a novel or news article, but rather split into much smaller chunks that you work on day-by-day to annotate and summarize and translate.
For a 100-line passage, we might split it into 25-line chunks over 4 days, and each day spend our time reading the section, circling, jotting down notes, writing furigana for the new kanji, and translating the vocab and new grammar. The entire chapter becomes interactive when each following page is understood to be a supplemental reference for the passage while you read it. Then after four days of picking apart the passage line-by-line, we used the fifth day to read it all at once like you’d read any book, summarize the content, answer the comprehension questions, then shortly read the kaiwa pages aloud to work on our understanding of conversational flow. A chapter per week is a very productive pace, I think.
Depending on the amount of time you give to the new vocab and grammar – adding them to SRS, coming up with your own context sentences to build understanding, writing the kanji out by hand, or none of that and solely experiencing them in the reading passage – Tobira could be a short part of a larger daily study routine or its own long session. In the classroom, our 25-line chunks would take us 4 hours, since everything we did was supplemented with making flashcards, writing example sentences, reading the section aloud, etc. But I’ve personally whittled it down to be a 30 minute piece of my greater self-study routine since then.
I wrote a longer breakdown of how we studied Tobira in the classroom over in the Wanikani forums (here). I was afraid I’d forget everything about how to study after I stopped taking classes, so I tried to be as detailed as possible to help my future self 
I hope this helps a bit, I enjoy learning from textbooks and having guidance for “where to go next”!
