Yes 66/79.
No there is no secondary power valve.
yes, 66 primary is stock, but remember you have massive high signal bell boosters from a dumptruck in there.
Yes, with the intake choice, jet 68-69.
Biggest issue with CJ carbs is the idle feed is very lean and idle circuit short. The bellboosters start early and a small high speed bleed helps it start even sooner, so little idle to speak of.
Idle airbleed is typically .079 and idle feed is .029
This works fine for a stock CJ or any engine that makes 18in at idle. If a large cam is used, drilling holes isn't the solution, opening up idle feed to .033 is.
yes the plates are available new, they are #172 for both primary and secondary.
One oddity of CJ carbs in general is by their very nature of how the throttle shaft/plates set up, you will expose more transfer slot than normal. This is part of why the idle feed can be set so lean. Part of this is the plane in which the throttle shafts are machined, and the thin plates.
A trick to look out for, the secondary plates are 172 and very very thin, this makes setup critical so you don't have an exposed secondary transfer slot.
I like to use the short vs diaphragm with these or often the secondaries will not fully open.
Personally? for a daily driver, these are exceptional carbs as is. You can certainly feel more low throttle torque with the bell boosters.