The journal itself would be a foreboding indicator. Instead of storm clouds culminating overhead, or an eerie music playing in the background that annoys the protagonist, he finds this journal. It's not stated until the MC confronts the antagonist that it is revealed to be his journal.
On the other side of things, I would put the journal in the secluded laboratory. Seeing all of the creatures inside the cages howling and snarling in the background while he reads this journal would add a bit of tension. However, i'm hesitant to do this since the laboratory scene already has a down time moment. The protagonist is running through the lab to find an exist when a creature latches onto him. This causes the main character to look at the saddened green eyes of the creature. The creature pleads with the reluctant hero to ends its misery. Because of the harsh experiments that were performed by the antagonist, the creature can speak an understandable language to the world's sentient inhabitants. However, the side effect causes the misshapen creation to be in excruciating pain. I made this the real scene where the reluctant hero questions his motives and if there really is such a thing as "going too far" when wanting to learn about the world.
It's not so much as the villain wanting the MC to find the journal, but for it to serve as one of two/three final straws that breaks the protagonist down. He realizes what the antagonist really is which disheartens the hero. The protagonist has really been alone since he wants to learn about the world. As he finds another that is just like him, this just complicates things as he sees these extreme measure that are taken to learn about the world.
This seems like the sort of question that would be easier to answer having read the entire book up to this point. Is this person you're submitting the story to an agent, or someone evaluating it - or someone who is planning to help you edit? If it's the latter, they are probably in the best position to give you specific advice.
Honestly, I'm not sure there's a "proper" amount of downtime in the strictest sense. I don't think it's all that uncommon to go on feelings and hunches. Ask a comedian how timing works, and they're likely unable to break it down. A lot is learned from trial and error or by feeling the audience. Sometimes there are set beats (or pauses) in routines, but you've still gotta know how long to sustain. Obviously, as a writer, you don't have the advantage of the latter, but that's where having your work read can help.
The plot of most novels can be pictured as a set of peaks and valleys, with the size of the peaks increasing as you reach the climax. So the length of downtime is going to decrease as you near the climax, while the peaks between are going to be more extreme. I'm not entirely sure from your OP if you're working in long form or not. In short stories, the trajectory is going to be more singular and direct. You don't have as many of those peaks and valleys, or everything is kinda focused on the buildup to a single peak, if that makes sense.
Not sure any of this helps, but it might give you something to think about.
It's hard to say in all honesty. I'm tying everything together into one larger story, but each chapter, minus a few, could count as a short story with them being between 3.5k and 7k words.
I guess either way could work. Although, I do want to maintain that smooth flow. Don't want the reader to feel like they hit a brick wall, getting dragged up said wall by a the rope connected to the harness on their back when they reach the transition phase.
Another problem maybe the transition phase being a rather long piece of exposition. It serves to give backstory to the protagonist's new companion, but does seem to ramble on the more I think about the paragraph. The main purpose of the antagonist conveying to story to the main character serves a couple of reasons. One of the large reasons is the antagonist wanting to grandstand, proving he is in control of everything no matter how the main character wants it otherwise.
Another thing is I want to antagonist to seed doubt into the protagonist since the reluctant hero can't believe a fellow mind would be so cruel to something. It's later in the story the antagonist is reference. The main character finds book in a library of a town/village that gives some information about his new companion, a rare bird. This moment later on is the shocker for the protagonist. He comes to understand that the person he wanted to respect is really his enemy, removing the last shreds out doubt that potentially lingered in his mind.
OK, so each chapter is treated as its own story, thus has its own arc. This is not an abnormal technique. I can't quite think of an example offhand, but I've seen it done in books before.
Might help to remember that the space between a chapter is a kind of transition as well. It's fairly common to have something important happen at the end of one chapter and then stop, pausing for the next event. Or to simply conclude an episode, implying some physical space or gap in time from that to the next episode.
I think using a scene in which less is happening in terms of plot points or actions as an opportunity for exposition or back story can be useful. The potential issue I see is being too obvious if it's framed in the dialogue, or having it feel pasted in rather than flowing organically from the narrative. The former is an issue with soap operas and that style of narrative. Everyone explains their motivations, which is not very realistic considering that most people can't articulate or sometimes fully understand what motivates them. They might not also want to reveal it, unless you've clarified the motivation in doing so. Otherwise, yeah, you get the Bond villain grandstanding when he could just be getting the whole thing over with.
With the last issue, it seems to me like you understand well enough what needs to be done. I think if the antag instills doubt, he really needs to appeal to something that matters to the protag, i.e. if he's a reasonable scholarly type, then make him question the validity of the scholarship of what he's read. Then the trick is to provide info that places the antag's claims into question.
Ya, basically each chapter forms a contained story. There are a few chapters which interlink between each other with a cliff hanger. This occurs in the first chapter where it leaves off with a cloaked figure standing above him to entice the reader to go for the second chapter. Used the cliff hanger method so readers can get the upfront meat and potatoes, so to speak. It helps to show them how the story will play out with later chapters and if they want to bow out they can. However, I leave them with unanswered questions and hesitation to really hook them in.
I'm hoping to have 4 arcs with 8 chapters per arc to set things up.
"Why can't 3 be part of the transition?
Honestly my solution would be to just write it, clear your mind, then go back and read it."
I really get the feeling it maybe best to eliminate the cliche "bond villain grandstanding" saint mentioned. Instead of the exposition section, I may just have the villain pin the protagonist to the wall. After that he gives a quick smirk/snide grin and would basically say to the reluctant hero, "did you like my journal?"
That acts as the trigger mechanism with the main character wanting to believe in his old ways, but forsakes them. He slowly accepts the fact that not everyone who wants to learn about the world has the best of intentions. There are some out there who care nothing about morality and ethics, and are willing to do whatever it takes to learn. I'll be re-writing another chapter and plan to reference the antagonist's words so that the protagonist really has it sink in that the person he thought was his equal is just an enemy with no honor.
Course I add another layer down the road as readers learn what triggers the antagonist to be this heartless monster, willing to do whatever it takes to learn.