Thank you, sincerely, for your response. The modeling process seems very intensive, but I have a true passion for my work and truly believe it will help many people.
Though I have already read and analyzed several papers in the field of computational neuroscience, the ones you provided are far more specific; I'll be sure to go through all of those thoroughly. Tutorials on the web will also be very helpful for learning the ins-and-outs of LS DYNA.
Regarding your last point, I will definitely have some form of mathematical intuition to predict what I should expect from my model. I am working with a mathematics professor at the Wilkes Honors College - Florida Atlantic University to develop a series of differential equations to supplement the model. Essentially, once I have a rough-sketch of the model created, one developed to the point where I can apply force to it and manipulate such, I plan to explain these results using a series of self-developed equations. My hope is to have the equations and model complement each other: the equations/formulas, specific to the dynamics of the brain's fluid movement inside the skull, can receive inputs that differ from injury to injury (mass of the individual, force that they received in their injury, angle/mechanism of impact, etc.) and provide a relatively reliable net output detailing the brain's total movement. The model can then be implemented to visualize these results, also being input-specific.
Of course, as you mentioned, I need to have a model-base to form a sense of intuition with, so I will get the model to a point where it is deemed appropriate by my research mentor to start 'equationifying' my predictions/results.
Once again, I thank you for your reply. It's helpful to know that thers have gone through the same process and that there's help to be found!