Thought I would tie this one off after a month of experimenting with AI. The biggest problem I was having that made my auto-traced sketches impossible to manipulate was the paths the auto-tracer was making. Despite having the paths scale set as low as it would go under the advance trace settings, the auto-trace was still making the trace overly complex. It would make a path for the outside of the stroke, the inside of the stroke, and a unifying middle path inside the stroke. But then it would jumble all these paths up at the slightest imperfection of my hand-drawn lines. This created a lot of anchor points and corner anchor points that were connected to the wrong paths.
To fix it I have to zoom in and follow each path to see where it is joined with another path that it shouldn't be joined with, and break the path somehow (mostly with the eraser tool). Or join the path with anchor points to the corrected paths. Or some combination of the two. The point is, once I figured out the settings on the auto-trace to give me the best trace, it still wasn't giving me very good paths to work with. For anyone else who has this problem with auto-tracing your sketches, just get very familiar with the pen tool and then zoom in to the paths of your sketch to fix them manually.