Just to summarize:
The CBU is 1/2" Permabase, not the 3/8" Permabase made for floors.
You will be using thin set mortar as the adhesive? Real thin set mortar come ONLY in a bag, it's powder you mix with water or in some cases an additive.
Shower walls are supposed to have a vapor retarder either on the studs or on the surface of the substrate. (Permabase in this instance).
Your CBU is already up, your only, (and I believe best option), is to install a surface membrane. I believe the best product is Kerdi, (the one I use), although there are others that work just as good. Another choice is a liquid aplied membrane such as Redgard or Hydroban. If you go with the liquid, be sure to read about the wet film thickness it should be. It normally takes 2-4 coats for it to work as advertised.