I didn't get around to the gui files. I got distracted with a big diff between 2.00e and SEP-3A.  I have a couple of observations:

intersection.cpp:372:  Used to be an if (!cont) instead of else.  Looks like this could potentially return false when it shouldn't.

world_tree.cpp:323-328:  What is the +0.5f for?  Wouldn't that move all the bounding boxes relative to the graphics?

I'll do the gui work tomorrow morning.