Did a bit of work today, though it feels like I'm back to where I started in a way. Here's the update:
-Tweaked the mouse support. Along the way Effectus hit the last straw as once I removed it to test something the mouse support was perfect, and the stutter problem went away completely.
-Dropped Effectus from the project. I already was planning on not using it on any future projects, but I had enough at this point as all the glitches I was getting with it that could not be fixed (or only had ad-hoc fixes) was making the game look poor. Went back to Theoallen's script. This though breaks all saves so I have no more saves for testing.
-Tweaked the Chapter 3 cutscene that I wanted to fix.
-Added proper mouse support to the Intro.
-Dropped fullscreen++. As I used 640 x 480 I noticed it upscales pretty well to 900p (what I use), and it will upscale nicely to the new 1440p monitors that are coming out by default, as 1440 / 480 = 3. Plus it didn't work well with mouse support, as when you go to fullscreen (or back) the mouse is in strange spots as it doesn't properly relocate it.