The PDF is helpful, with its use of images and charts. The proposed method of drawing lines seems to be consistent, and seems to yield the start of a message. The author says they could only get a solution from some of the paintings, so the solution is incomplete.
It doesn't address much of the other data that people have found, such as numbers and colors and letters (oh my!), which leaves this feeling like a dead end for now.
Great job Justin, a lot of great work. Unfortunately, I have scoured the lighthouse grounds and there is absolutely nothing there. With that being said, I do believe the lighthouse plays a role but only as a point of interest. Keep up the great work, you put a lot of time and effort into your solve. I live in Maine and have been working on this hunt for a month and a half. I can't believe how much I have learned about MDI. I actually worked at MDI hospital for a short spell. Anyhow, if you have any other ideas or thoughts let me know. I have many, but much simpler and straight forward.