Hi Aaron42,
One area of research that may help you in answering these questions or coming up with a project is to research patients who have had Strokes. A stroke occurs when there is a blockage of blood to the brain (ischemic stroke), or when there is an injury to the brain and blood vessels break (hemorrhagic stroke). I know about this stuff because I had a stroke when I was 28! Something I know for certain, based on experience, is that my nervous system, and thus, my muscle reaction time improved over time. When I first had the stroke, I couldn't use the right part of my body at all. But because I went through physical therapy, I 'retrained' my muscles and 2 years later I had a full functioning body. I still have some numbness in my hands and feet, that I will probably never get back. But my gross motor movement is excellent. So, yes, it is possible to retrain your body, muscles, and brain to increase reaction time. The brain tells your muscles and nerves what to do. What is the relationship? That could be a good question to explore.
http://www.fi.edu/learn/brain/exercise.html
There are diseases that affect the nerves themselves (not the brain), that can decrease a person's reaction time, or eliminate it all together. One way that scientists find out how the body works, how the brain works, is by looking at patients who have an abnormality, such as a brain tumor, a musculoskeletal disease, a stroke, diabetes, etc. Maybe exploring a pathology/ disease would be a good place to start.
http://www.ninds.nih.gov/disorders/brai ... _brain.htm
Did you know that the younger you are the better chance you have at stroke recovery? Also, the idea of "use it or lose it" holds some truth, why would that be? There is new research that demonstrates that nerves can adapt and form new pathways (not healing the broken ones), which may restore or help in nerve function. Try looking up information on Neuroplasticity. Here is a website to get you started:
http://faculty.washington.edu/chudler/plast.html
Hope that helps. Please post here again if you have further questions.