I would say that CSE is the most prepared, in part as a lot of their planning has been good and a lot of their open reporting on what they've been doing has been fantastic. It's largely that the connections between CSE and the CAF are almost non-existent. It's very informal, from what I've been able to learn.
There needs to be an actual formal command structure in place to mediate what happens in the event of a conflict. Right now what is likely to occur is that it's going to be given to CSE to respond in an active cyber-threat. I believe that there are more formal connections in relations between CSE and Global Affairs than there are between the CAF and CSE.