HHmm, we are lucky we are both building Cobras otherwise we would be ENEMYS! BA Pursuit ute here with a Vortech and some other work here.
I am using an Autronic SM4 on my Cobra. Actually I forgot to give you the most important link concerning Cobras & 4.6 modular engines.
www.ffcobra.com
Then find the 4.6 roadster forums there. There is a dedicated modular section with plenty of info. Plenty of wiring diets that you may want to look into!