But you've done exactly what you were supposed to do! I bet this post took you fifteen minutes to write, and it reads like you were gathering your thoughts as you went.

Here's the climax:
So long as Jude realizes Edward is innocent, gets to Daniel Aberforth on time for the Priest to die, and then notices Aoife trying to spy on him...the other stuff will depend entirely upon Jude.

You also said something key here:
So this means that Edward took a day, maybe two to run from Italy to NC remaining undercover the entire time (this is a world with airplanes and whatnot, so it's not like he literally ran).

This demonstrates exactly why we add timelines to our outlines - to identify, in advance, what's chronologically possible, and what's not possible. We don't want to get to November, crank through the scene where the church finds Edward in NC, and then realize - CRAP! How did the church find Edward in six hours? You can't even FLY to North Carolina that fast.

The exercise is meant to help you identify the spots that might cause chronological trouble later in November, and you have clearly succeeded.

Cheers,
Michelle