Quite frankly, The connection between practicing medieval stone masons and the modern Masonic fraternity isn't well documented. The best documented link between the fraternity and practicing stone masons can be traced to Scotland during the rule of James VI when his master of works William Schaw established what became the modern lodge system around 1598. Schaw reorganized the existing craft masons in Scotland into a lodge system that was directly under his oversight and established the apprentice/fellowcraft/master mason system that modern Freemasons still use, as well as the codification of ritual and systemic record keeping that prefigures the system lodges use today.

There are older examples of organizations focused around craft masonry, but they don't really have the obvious connections to Freemasonry that the Scottish lodge system does. I won't have access to the book until I get home later, but if you have other questions, I'll be happy to try to answer them.

Source: The Origins of Freemasonry - Scotland's Century, 1590 - 1710 by David Stevenson