I believe these are simply changes to the content of these adventures so that there is a single plotline that connects them all. As that is completely mutable, there is no way to get it "wrong." It's not like converting to MM3 monsters or anything mechanical which might upset balance. So I wouldn't worry about it. "Bridging material" between modules is an excellent opportunity to collaborate with your players on how one adventure ties to another. It will make more sense to your group and, since you're using the players ideas, will engage them more thoroughly than worrying about exactly how one mod connects to the next in your notes. I cannot in good faith recommend anyone use plot-based preparation for adventures anyway. If the DM wants to write a story, he should just write a story and email it to his players. If you want to use the RPG medium for its intended purpose of creating stories collaboratively, plot-based preparation is only going to get in the way and will be more potentially wasted prep to boot.
