Where does the presumption of constitutionality from? Is it a logical extension of the presumption of innocence or does it derive from English common law... or is it just something they made up in one of their rulings?
No, it has nothing to do with the presumption of innocence.
The first case I cited, Brown v. State of Maryland, 25 U.S. 419 (1827), is from 1827, so the principle has been around for some time. Looking at the opinion in Brown the Court doesn't say anything about its origins -- merely that, "...it has been truly said...". So it sounds pretty well accepted in 1827.
This could be an interesting project for a law student who wants to write a law review article, but the doctrine is so well settled by now that its origins are pretty much moot.