KoK, you’re spot on that it’s the first two and a half seasons (up to production code 3.06) where the chronology is wobbliest (hell, check out the production codes on Wikipedia compared to the release/chronological orders before and after this point). So it’s really this early period that needs the most work. And after that point, there are very few one episode arcs, so absolutely minimal merging to do.
Cloak/Lair would definitely be the most straightforward way to present Lair, unless there’s a way to integrate its best elements with a more Grievous-focused episode.
As for the chronology, I’ll respect canon in terms of the idea that all these events happened as written, but I think for the theoretical audience of this project, so long as there are no obvious causology errors presentation must come first. That said, I don’t expect to break anything.
People are going to come into this show wanting to see Mandalore and Maul, so I think it’s really important we get those plotlines running early, and keep their presence felt throughout.
I think this best serves the audience who are coming to this show now. Of course, on the issue of chronology, this is merely a matter of presentation, so people like yourself with other preferences will simply be able to reorder episodes.