Jerry - I wouldn't put so much faith in innercoolers running a pressure box and a carb. Been there, done that. (for sale: Vortec custom built water to air innercooler for a 600cu/in motor, cost 1900$) The real trick for a street blown engines in pressure box situations I've found is to keep the temps in the top of the engine yet control the overall cooling engine temps. Pressure box situations are completely different, and note I didn't say better, but I believe that to be so. And this stuff is not in the standard hot rod books either.
Your correct, fuel injection does change all of this. And you are further correct that the engine should be custom built w/stronger parts to include the cam grind for blower motors, though time and again I've seen mild boost situations work long term with factory engines. I've found that most of the blower type guys on this site know this stuff, know and do this stuff. You see, Cobra guys are not your typical hot rodders I've found, a few even have a few dollars that they can spend on insane ideas.
Welcome to the site - and be prepaired to be disputed a bit, you see that's another characteristic of this Cobra crowd too.
Cobrashock