It should be noted that Trail of Blood is historically inaccurate. Granted, I'm taking the word of my evangelical seminary professor on it, but in more nice terms he said it was more of a propaganda tool than something reflecting a critical understanding of church history. Being that the early church had apostles and prophets, and Baptist polity has no such thing... that should be enough to tell you there is not some unbroken continuity.
If you want some good reads on church polity, though I don't always agree with the ultimate conclusions many of these guys make, I'd check out the house church movement. Most of their writings I've found to have a great understanding of these things.
Plurality and equality of elders, all the gifts of the Holy Spirit being for today (including apostles and prophets), consensus based government, an "open church" where every member can contribute in a service because of the universal priesthood of every believer. Being cell/house based instead of based on a large gathering. etc