Stock intake will work fine, maybe massage the divder a'la Jim hands book, which if you haven't picked up you should. The Q jet will work great if rebuilt well. If you're willing and have some experience you can do a pretty god job following Cliff Ruggles tips in his book- yeah this is the other "if you haven't picked up you should" tip.
16 heads are good, simple porting and gasket match will help a bit. RA manifolds beat out the stock Logs and may fit easier than headers. More stock looking too.
I just looked into a cam for my new motor build and Butlers suggested a XE268 for my "stock" 428 rebuild. Specs are a cross between the RA III and IV.
But your situation maybe different than mine, I've got a M20 tranny which is more forgiving then a AT
Have you or are you joinign the Rochester POCI group?
I'm in the Syracuse Six Nations POCI club and theres usually good people there and lots of advice/ experience. Pontiac Jack on here (PY) is out your way (Phelps).
Several guys from Roch came to Syr for our Spring show and several guys from here when to Webster for the Roch show. I hope to do that to this year.
My motor should be done this week but not sure when it will get installed. Sometime before the first ESTA test and tune in April I hope
Howard