Which engine should I choose?

[Tengu]

Welcome Hugh !
I guess it really depends on what you want, a customised cobra or one that has an original look. If you're going down the aluminium body path, I suppose you might be looking at the latter. If that's the case Fe is the way to go, but to be honest, because we're in Aus, it's a choice that will be expensive and there are very few Fe experts here.
A 427 Windsor stroker is an alternative if you want to stick with a Ford engine and are looking for that magic number.
Having said that, I would seriously consider what paintwerks had to say. So many members are really happy with their chev engines and can offer you some really good advice if you go that path.
I have an LS3 in my daily driver and love it, that would be a great engine in a cobra. I just really enjoy the rawness and sound of the big block ford. That's what I like and I wouldn't go any other way for my cobra, being LHD and looking very much like an original one.
if you weren't building, what would you buy? Have a look around and when you see a cobra you wished you owned, then build one like that. Pace are looking good and there's a few engines out there that are better than Fes
Best of luck
Mike