A mystery with 3 subplots

I'm writing a branching mystery novel. It's more Raymond Chandler than Agatha Christie: the mystery is a driver-of-plot rather than a puzzle for the reader to solve. Following modern cop-show/detective tropes, the various suspects are involved in 1 of 3 hidden subplots. Over the course of the novel all 3 subplots are revealed piecemeal through the investigation.

My question is specifically about how and when (narratively) the 3 subplots should be revealed to the reader.

Counting the clues

Within each scene there are clues that can be uncovered, revealed through dialog with suspects. The reader has the chance to uncover 2 out of 3 possible clues in each scene through the choices they make. (What I didn't realize when I started this structure is that no matter how the reader chooses she will not receive all the clues, hence it is not really a fair puzzle-mystery.)

In my prototype, I've connected the discovery of each clue to a (behind-the-scenes) bean-counter. Finding a clue about Plot A will add 1 point to the counter that tracks Plot A; finding a clue about Plot B will add 1 point to the Plot B counter, etc. At the end of each Act, I tally the score to know which of the subplots the reader has learned the most about.

A simple 4-act outline of the novel:

Act 1 – Introduce the suspects and their involvement to the crime
Act 2 – Re-interview suspects and address inconsistencies
Act 3 – Eliminate 1 suspect (found murdered)
Act 4 – Discover and pursue the culprit before other suspects are killed

What is the purpose of the branching narrative?

This isn't strictly CYOA. The reader has influence over what questions the detectives ask, but major plot branches surrounding the crime are decided by the novel itself. The culprit is picked randomly, as are the victim(s). The goal is a dynamic detective story where the outcome is undecided.

Essentially, all the suspects have secret agendas for the detective to uncover, meanwhile they each have an extra level of their story that unlocks if they are revealed as the killer. The mystery is setup so that all of the suspects "fit" the initial crime. Up until suspects begin to be eliminated by murder, the novel doesn't need to assign a guilty character until more than halfway through. (It's also possible to decide the murderer late in the story to best suit the narrative that has already occurred, ie: deliberately choose an over-looked suspect, lead the reader astray then create a dramatic twist, etc.)

Which subplot is favored?

Here comes the question, and it's more about conventions of a mystery narrative than a game mechanic. I can use the bean counters to learn which subplot the reader is currently pursuing, and alter the clues that are being shown to make sure the reader is getting the all the important information.

I see two options, but I don't know which serves the story better:

Balance the clues, so the reader gains awareness of the various subplots in equal measure.
Weight the clues, so the reader sees one subplot more than others at a time.

In the former, the novel becomes "self-correcting" and presents the 3 subplots early and more-or-less equally. The narrative doesn't favor any one suspect in particular. If the reader has learned too much about Plot A the novel will deliberately start showing clues from Plots B and C, so they all progress in tandem.

In the latter, the majority of the clues will slant the mystery to one subplot (per act). After a few scenes, the novel sees which branch the reader has discovered more of, and begins pushing clues to fill-out that plot first. At the end of the act that subplot is deemed to be a red herring and the next subplot is favored (the murderer might still end up being a suspect from a discarded subplot by revealing a twist, so it is not necessarily a give-away of the ending).

A third option is to do nothing and let the clues and the plots fall where they land based on in-scene navigation. Inevitably one subplot will have more details discovered, but that's the nature of a branching narrative.

The Question

Since the branching novel is aware of the clues the reader has uncovered, should it "lean in" and favor the dominant subplot (changing focus at the next act), or should it carefully build all the subplots concurrently so as not to predispose the reader to a single red herring?

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