ERA recommended that I paint (or have coated) the entire undercar exhaust system satin black, as it helps to de-emphasize the visibility of the system. I plan to do so.
The 390, 427, and 428 V8s are all identical from the top (which is all you can see once the car is completed). And, a 390 V8 built for reliability and durability is plenty for this car--it shares the same stroke as the 427 so it will rev (and with less reciprocating mass than with a 428 or with a stroked crank), but you'll still have more low-end torque than most people can effectively use. The Toploader 4-speed adds to the original feel. Both will save you money, and you'll be able to comfortably drive more than a quarter-mile at a time
By the way, the original 427 Cobra prototypes had 390 V8s (albeit in aluminum) and the inboard-mounted rear brakes that ERA uses even today on their standard rear suspension. The only advantage to the outboard brake option is improved cooling for those who spend a great deal of time on the track, which does not seem to be where you are headed. Otherwise, that option increases unsprung weight, a disadvantage for those of us who like to drive on regular roads, highways, and mountain passes, which does sound like what you want to do.
With regard to wheel size, the original street models (whether 427- or 428-equipped) came with 7.5 x 15" wheels front and rear--that was part of the original look. The 9.5" rear wheel widths were original only on the SC models that were built (about 50 of them, according to some authorities).
Your plans for your car sound great, and the final product should make you happy. All of the rest of us have our biases for why we did things the way we did, so just accept what we say simply as "food for thought."