When comparing the 5.0L windsor to the new Ford DOHC motor, you have the width problems that Les mentioned. They are bloody huge in every way.
Depending on budget, if I were building a new Cobra now, it'd either be a turbocharged Lexus DOHC (like Scott OZVENOM), or a supercharged LS1 (like Garrett JUSTBETTER).
...... or I'd just say to heck with emissions and fit an 8000rpm, 410 cube 13:1 compression Sprint Car motor making 800+hp !!!