My current plan is to do COT2 in three sections.
The first section will comprise three books, and will consist of 12 to 14 short stories. I say 12 to 14 because I have 14 ideas for stories, but at least two of them are so distinctly independent from the grand plot arc of COT2, they could easily be omitted. Five of the stories happen before COT-R, and the other nine after. Of the nine after, four of them build upon events of the previous ten stories. Does my math make sense?
The second section will be a stand-alone novella featuring Ghost and Lytha in an adventure that, while being a naturally progression of their story, is not intrinsically linked to the grand plot arc of COT2. I decided to do it this way because I wanted to continue their story, but I felt that trying to integrate it with the main one would be a disservice to both. I am not sure if I want to tell it in the COT-R standard four-chapter format, or go for something different, but it will be a stand alone story about as long as one of the COT-R books.
The third section will take the plotlines introduced in the first 14 (or 12) short stories and weave them together into a two-part novella (Books 5 and 6) in order to bring COT2 to a conclusion. It will strongly resemble COT-R (and COT for that matter) in that it will be telling multiple stories simultaneously, forgoing the short-story format used in the first three books.
I feel that doing it this way allows me to focus on the small issues for the first three books, in a series of stand alone stories any of which could exist separate from COT2 (or even Thief canon). Then, I switch from crawling to walking with a much larger-scale stand alone story, and finally wrap it all up with a tale that readers of COT-R would be accustomed to that can launch directly into the meat of the plot without having to spend several chapters setting the stage. All of this also assumes that COT2 will be about the same length as COT-R, but it's flexible enough to allow anything to happen.
In a nutshell, COT-R was one book in six volumes. COT2 will actually be six books. The first three will be short story collections, followed by a novel, followed by a two-part novel. That sounds doable, and fun.