First of all, WOW! 8D
I really appreciate you going through them so thoroughly. I went ahead a fixed the problems you mentioned, and a few more while I was at it. Besides what you mentioned, a few waypoints were only using one-way connections when they should have been bidirectional, while a few others just had plain bad connections. I also fixed a few problems with some radii, among other things. So you don't have to go through it all over again, I've attached a large, rather artistic collage of screenshots of a few of the things I fixed, along with the new waypoint file.
Oh, and everything you suggested works beautifully. As though that's any surprise. 9_9
