Hello Chuckster,
I have had four Cobra roadsters, one Daytona coupe and one GT40 each time the one I ended up loving was the one that had the "Old School" look as close to the original cars that I could get.
#1 Build what you want the first time.
#2 From the top the 390, 428, 427 CO and the 427 SO look exactly the same. If you want the old school look it does not matter, if you want to be truthful to the question is it a "427" like the badge on the side says , you need to have a 427 Roush, 427CO or 427SO ---- you choose.
#3 You have the ability in your right foot to get as much "Punch" as you want, with a light car like the Cobra any of the engine choices will give you great cruising and a lot of push into the back of the seat when you punch the loud pedal.
#4 Resale ---- There is always a buyer for any ride, build what you want now and let the future take care of itself.
One man's opinion but, based on having made the mistake of economy over desire.
BTW --- I have CSX4264 with a 427 SO in the garage parked beside my GT40 with an "Old School" look engine sitting behind me. Lots of pics in my gallery.
Tony R.