There are hints of things, but nothing really changes for the new stuff until after you finish the original adventure. I'd probably consider more changes, but I have to think about that. Luckily I have a few weeks before we start.....
There is no reason not to include other side quests, imo. Things pick up when they reach a certain level, really, because the story up until then doesn't really feed into the new story. Which, ya, now that I've typed that, I'm likely to change more and clue the PCs into ....sure, you have to do these things, but something bigger is going on....