My work in progress is in a state of disarray and I desperately need help.

So I'm writing a story to be published by a publishing house, no self-publishing. And I've just started writing it, having received guidance from a fine-tooth comb editor who has carried out an in-depth analysis of the work. I've got the plot, structure, character arc and first drafts showing what I've in mind. But the first drafts are in a state of disarray. Now I need to rewrite everything, having in mind the first drafts and then apply the changes given to me by the publisher in the following phases of the manuscript. <br><br>To do so I need a good first draft in order to be able to rewrite it, following the changes given to me. The problem is that in the first drafts there are a thousand things, for instance some chapters are in the wrong place, some scenes are cut off from the plot, there are a thousand recurring themes present in the first drafts and there are a thousand contradictions between one scene and another and then I need to apply the changes given to me by the publisher in the first drafts before then applying them to the second drafts.<br><br>In short, I'm mad, for I don't know how to organize and rewrite the work following the first drafts and then organize and rewrite it following the publisher's correction. But, above all, I don't understand how to use the first drafts to find a central idea to then apply to the second drafts. I mean, I should create a timeline to organize the scenes and then I will have a central idea. But I don't understand how to create it because in the first drafts everything is in disarray and there are a thousand contradictions among them.<br><br>I would therefore ask you for strategies, advice, references or video courses, suggesting how to organize and rewrite a work in the state of disarray.<br><br>Thank you.<br><br>&#x200B;