After all those upgrades. With the stock 2-barrel carb and intake (and exhaust man.), I don't think you will notice much improvement, if any. Ford's stock exhaust manifolds are pretty much anemic as well. I would definitely also include a new intake manifold and 4-barrel carb. Weiand Stealth, or Weiand Street Warrior intake. If you want stock, find a stock cast iron 4-barrel intake manifold. Summit Racing's house brand 4-barrel carburetors are modeled after the Ford Autolite carburetors, so look similar. I'd also look into short headers.
Instead of spending a lot of time on those cylinder heads, look into a pair of 1969 351W cylinder heads with the C9OE casting. Larger ports, valves, and valve springs without all the additional work and money. They have a 60cc combustion chamber, so double check your compression ratio.
*** I mention these things because, keep in mind, regardless of what motor you build, it will only be "period correct". Numbers matching is gone as soon as the original engine is removed. Unless you find the original motor, it will no longer be numbers matching.