Easy WayPoint System - Character climbing at waypoint

I am hoping someone can give some insight as to why my character wants to touch a waypoint with it's feet instead of walking through it and head to the next waypoint.

I have attached a video showing a small example of what I mean and placed the controller script I use.

I initially used a Capsule per their demo and it worked as expected. But for my purpose I wanted to have an animated character to follow the path.

The capsule required that I placed the waypoints above my scene around -2.21 (see screenshot) and the capsule would go to the waypoint and turn towards the next waypoint and continue. However, when I use my character and have the waypoint up like this it wants to walk 'in the air' and touch the waypoint with it's feet. Then goes crazy.

When I place the waypoint under the road (screenshot) the character will continue through the waypoint, but not without pausing for a tick and stutter. Often times it instead rotates on all axis instead of continuing through.

view the video here. I couldn't attach it.

Small example showing character stutter and then toe touching.

WaypointMover.js script used to handle waypoints:

EDIT: you can download script for viewing (less lines) WaypointMover.js file

I was able to narrow down where it goes haywire.

in the js file, start at line 302. I enter the SmoothFacing condition and begin calculating my rotation. I read somewhere that since my character has a rigidbody attached that it can sometimes mess up what I am doing here because does the same thing.

Apparently rotation calculations become off after the first few waypoints. My rotation variable went crazy when viewing the output messages.

Finally, here is a pic showing my settings for the above: