Since the engine isn't installed. I'd keep the basic long block, as is, with the exception of replacing the cam. Since your considering the CJ heads, you shouldn't be concern about the head cast # so, by that you can get a set of C6 - R heads and let Blair work his porting magic on them (~300 cfm) go with the C7 - F intake, CJ ex manifolds 2 1/2 pipes, +/- 735 cfm carb.
I think that might get you the most bang for the buck.
I dislike cast iron manifolds, even the CJ and weighs more than most all FE intakes by about 10 lb.
I'm going to drive the car over the summer to see how it performs, but will have the distributor recurved as that's fairly simple. As noted earlier, this isn't for max performance, but good reliability with some bump in power. As I want to keep the thermactor system (for originality), that leaves me with the stock GT390 or CJ heads (from my understanding).
I'm a year out from going through an engine refresh, which gives me time to start looking for parts. It appears to be a challenge in finding from a trusted source...especially the heads. I have the challenge in finding a respected engine builder as I'm in Colorado, and need to get the engine to them while trying to keep the downtime to over the winter.
Obviously keeping costs in check and "bang for buck" are on my mind, but I understand a quality rebuild with good parts and having it dynoed / broken in will cost...something I'll have to work on with a builder.
For now, I'll start looking at the F427 or PI intake, and maybe the CJ heads. I'll also have to start looking for a builder at some point to discuss the internals (head porting, cam choice, etc.).
Thanks for the assistance / advice from the group.