Did you check any of the bordering wilderness cells to see if that was happening on your end?
No, I didn't check because I really don't think it matters. Since once you have all this "working" again, I figure you will go back and make your navmesh edits, they are going to get flagged as "dirty" anyway. Being flagged as "dirty" or edited, isn't a problem in itself and nothing you can really do about it when you make an edit.
What I did test was that the intro worked. After I read your post, I went back to the original ESP and started over. Each cell cleanup got me farther through the intro, until I got tired of it and just reverted the remaining cells. After doing that, no CK crashes and I could get all the way through the first quest and in to the keep.
I don't remember now if the Pathfinding warning came up, but regardless, it's going to when you make any edits in the cell. And from what the Beth dev said, it's "just a warning". Unless you are not going to make any navmesh edits in those cells, you wont be able to avoid it anyway.