While it sounds like the OP has a more generalized problem, I find that the WotC full-book release published adventures are particularly cumbersome to run. Basically I think they have more moving bits and pieces than the creative team can keep track of amongst multiple authors and though multiple revisions, and that by the end product you have lots of stuff whose purpose is obtuse, subtle, or missing, which makes trying to rework it even a little without gutting it wholesale an exercise in frustration. Of the ones I've attempted to use Out of the Abyss was the worst offender as it lacked even the introductory chapter summarizing the adventure that some of the other releases have, making for one of the most difficult to follow works of fiction I have ever encountered. But even when there is a proper introduction the adventures are still often written in a way that seems designed to not tell the DM why things are the way they are. This might be fine for a DM rigidly following the book, but most people want to make it their own at least a little.
I really just think larger scale adventures should include marginalia pointing out everything consequential that comes up whenever it comes up, and pointing to when and how it is of potential consequence.