Thanks for the post! I just checked out the article, and it looks great! Logistically, it might be a challenge. If I work out at off times, it could work at my gyms. I plan to give it a try, as this is the type of program I enjoy doing.
I have, in the past, done things like you are suggesting (substituting BW moves for barbell lifts). The trick is to find something equally challenging. I'm pretty good at BW stuff (and I think you probably are too), so that opens some doors. For example, feet elevated 1 arm push ups for heavy BP. Three of these are hard. Hand stand push ups with hands on boxes so you can go deeper, for OH presses. Pistols squats (even weighted with KB's in your hands) for front squats. Single arm DB high pulls or snatches to replace the barbell lifts.
These aren't ideal. For the unilateral varieties, you'll end up with more sets obviously to work each side. The explosive DB variations of high pulls and snatches aren't as heavy as the BB versions, and again you'll do extra sets to work each side. I would think if you start with one alternate variation, you'd want to stick with it a while and allow for progressions with the same moves.
As for the last two questions: He does state in the article that you cannot do the exercises separately, and the circuit is key to the program. Lastly, he shows a video clip of him doing one circuit to give you an idea of rep style. He doesn't emphasis the eccentric, and instead performs them fast and explosive.
Not CT, of course, but thought I'd chime in.