Gary Dryfoos, apparently still of MIT in Cambridge, MA, who has been collecting and disseminating information for about as long as there has been a World Wide Web:
http://web.mit.edu/dryfoo/Masons/
Grand Lodge of British Columbia and Yukon has been keeping excellent material on the organization for almost as long as Gary has:
http://freemasonry.bcy.ca/textfiles/history.html
Overview of the history of Freemasonry by the United Grand Lodge of England (sometimes described as the "mother" of all "regular" grand lodges):
http://www.ugle.org.uk/what-is-masonry/history-of-freemasonry/
The Quatuor Coronati Research Lodge, regarded as the leading resource in the world for Masonic information.
Philalethes Masonic Research Society (almost could be described as the North American version of the Quartuor Coronati Research Lodge):
https://freemasonry.org/index.php?option=com_content&task=blogs...
(For some reason, it comes up as a "dangerous page" on my browser, but this is the actual site.)
More or less reinventing the wheel here... may as well just give you Gary Dryfoos' research links page:
http://web.mit.edu/dryfoo/www/Masonry/Pointers/pubs-libs.html
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And a note on collaboration with your local lodge:
For a group that describes itself as a "society with secrets" (as opposed to a "secret society"), you'll find that Masonic lodges are very open about their history. They cannot really talk about the rituals and current business that go on inside a tiled lodge (the rituals are quite benign, that much I'll say), but they are often very interested in working with researchers (providing information, etc.) who are not lodge members, even on topics as controversial as the "Morgan Affair". If you are lucky enough to be in Boston, you have an excellent resource in the Samuel Crocker Lawrence Library at the Grand Lodge of Massachusetts building on Tremont and Boylston (T-Station on the Green Line: Boylston). But most Grand Lodges (especially New York) have research organizations that are trying to uncover their own histories and would welcome the help from those who have ancestors who were Masons.
The list I've given is pretty much made up of either people who are Masons, or Masonic organizations. Most anti-Mason sites seem to be pushing either a political or religious agenda, and I've yet to find one that is particularly helpful on actual history. In a way that's kind of sad, as the Anti-Masonic Party of the early 1800s did, for better or worse, contribute a lot to the shape of politics in the United States, almost (but not quite) as much as Masonry contributed to politics before the Morgan Affair. But most Masonic researchers, other than with regard to rituals and current business, are generally very open and driven at getting to the reality on historical matters, even on the very few matters that aren't as flattering to the organization.
Excellent project selection, by the way. -Ben.