A rambling narrative can be executed very badly or very well. Maybe it's tool to give color and depth to a world, but it can simply be a sign of an unfocused book. In all cases, what's important is how the reader will react, and that can be tough to estimate. It matters not a bit if you've planned the book out well if the reader believes you've given them the equivalent of notes tossed into a paper bag: They'll close the book and move along.
Do your troublesome plot threads give the reader critical data, or details that will add to the world of the novel? If so, then these scenes are needed. (You've already established that this is the case.) Next, you'll need to make sure the reader has faith in your storytelling. Will the reader find these scenes interesting enough to continue through pages that are apparently unrelated to the story? Unrelated detail can also become interesting unrelated detail when it's tantalizing. But presenting a reader with interesting baubles repeatedly will get them used to shiny things, and again they might give up on the story.
Discontinuity, to me, means a feeling of things not adding up. And dull-as-dishwater characters will turn readers off. But readers have a memory, and they're quite capable of feeling many things at the same time. Before they get to this point, do readers also sympathize with the characters and the situations? Do they find a character lacking in interest, or do they want them to grow and improve as people?
Getting readers to care about your world will see them through the desert of dullness, but it'll be easier to propel them across the dunes if these "desolate" scenes are shorter and interspersed with more accessible material. Unless you have a very good reason to have all the difficult scenes as a unified central section of the book, consider resequencing these scenes. Perhaps some scenes containing critical color can be removed, any information from them that the reader needs embedded in earlier or later scenes. The rest of the middle-section scenes could be preserved and interspersed with action.
For an example of this done well, any of the Bas-Lag books by China Mieville will do, but Perdido Street Station is a particularly good example of the impenetrable character, performing actions whose intent and meaning are utterly opaque.