Yeah, sounds like you have a plan. I think the only way to retain sanity is to add books in a very disciplined fashion such as by author or series as you suggest.
My original plan was to just "get everything in there" and then clean it up. Unfortunately I keep getting distracted by writing plugins etc so my backlog keeps growing and I am betwixt and between...
I think I need to change my approach - I've written tools that do a lot of preprocessing outside of Calibre to workround the issues somewhat but it's really only bandaids and delays the inevitable. I think rather than the goal of getting everything into Calibre first, I will just start afresh with a new library and do author by author starting with the ones most likely to be read first. I'll obviously still have an enormous duplicated mish-mash mess of books for everything not yet processed, but I had that anyway before I found Calibre