A Messy Mesh overflows the Mesh Masher (collision detection)

Upon implementing collision detection with GIMPACT (the package used by Bullet)  in ODE, our physics engine, the results were highly unsatisfying. It runs at sensibly the same speed has OPCODE (ODE original collision detection package) and it also crashes with a stack overflow if the complete bioloid is added to the collision detection scene.

When this problem was investigated it turn out that the problem afflicted ODEs sample bunnies also and not only our simulation.

However, upon following a topic found online it was  revealed that the cause of this crash was the meshes inside the meshes. Meaning the bunnies were inside each other and the collision detection algorithm behaves very poorly under these circumstances. The collision detection expects meshes that represent the colliding area of an object, meaning only the outer edges of it. For instance, this simulation has more bunnies and it does not overflow:

Returning to our model, we realize that the SolidWorks exported mesh is very messy. There is excessive detail and many interior triangles (the kind the collision detection algorithm does not expect). In the following image some problems are highlighted but many others are present in the image:

The solution path to this problem is a simple yet a hard one, the editing of all problematic vertexes to achieve a good behavior when inserted into ODE.