I removed the old collision detection manager from the project and removed all references in the code. Added a quick test collision detection routine and it looks like it is in the right spot. I did notice that it doesn't complete destroy the objects with the calls I make. I think I've forgotten to remove both objects associated with each displayed object from the physics engine, instead only removing one.
Also, I noticed some odd behavior in a couple of places and made some notes in the code. I also found an issue where it crashes when it tries to create a new growth in a location that one had already been created. The way it is being stored was because I was doing all my own collision detections, so I should be able to simplify that area.