I think it's a bit of a learning curve finding your best method and it's quite personal and depends on the book too.
I have found that I write quite organically so I prefer pen and notebooks for the first draft and any planning, research etc
I have a notebook with blank pages that I use for notes, ideas, bits of writing that might fit at another point in the novel and work things out in there. I do a mixture of timelines, flow charts, diagrams, questions I ask myself (on behalf of my reader)and jottings. Move between this and my lined notebook. In the lined notebook I write a rough initial draft on alternate lines and use the margin for annotations.
I find it's much easier to write when I have a good idea of the purpose of the scene I'm writing so I am tightening up my planning in my other notebook as I go. I work as though it's a puzzle with clues and I keep a check on whether it is working as I go along. However, if I feel stuck I do write the continuing story in the lined book even though I know it's not the best of writing it will be changed later but often doing that frees up my thinking.
So I am working on two time periods and ask myself questions. Such as (made up example) I want Kevin (main character) to meet Sue at the isolated farm, where they last met 20 years ago. But why would he go there now after all this time?
I do this brainstorming part in my notebook with my diagrams, thoughts, on motives, character and then when I'm happy or sort of happy I carry on with writing Kevin dropping everything and rushing off to the farm to see Sue comfortable in the knowledge that he has a motive for it that I think is plausible and suits his character and the story.
I doubt this is helpful and probably doesn't answer your question. I think more people use tech to help so that might be something to consider.
Try a bit of everything until you feel you are motivated and back on track. Also reading similar books to yours is a good way to feel a new buzz and inspiration. Good luck! It sounds like you have lots of material already.