David,

This is a great question. Let me offer you what little insight I've gained into the field.

To observe neuronal changes in Parkinson's from exercise, I would first take a look at the connection between exercise and dopamine production.

http://www.mdpi.com/2076-3425/3/1/39

SPECT and PET scanning have shown to be effective in scanning for dopamine transporters. These should show up in the substantia nigra. Doing periodic scans throughout an exercise program would produce interesting results.

http://www.ncbi.nlm.nih.gov/pubmed/14531039

I think the aerobic approach is beneficial for the neuronal and neurovascular changes associated with exercise-induced hypoxia, and there's great evidence out there for these types of changes.

ftp://217.219.170.14/Sports%20Group/Other%20Prof_/Shaahandeh/training/43-PROLONGED%20EXERCISE%20INDUCES%20ANGIOGENESIS%20AND%20INCREASES.pdf

http://integrativehealthconnection.com/wp-content/uploads/2011/11/Exercise-experience-and-the-aging-brain.pdf

The goal-oriented nature of your proposed exercise program would seem to provide additional upregulation of the dopaminergic system, presumably through the remodeling of reward pathways. The change is predicted to be localized in the nucleus accumbens and ventral tegmental areas. This is more along the lines of the "internally triggered" mechanisms you want to focus on.

Dr. David Linden wrote an interesting article for Psychology Today on exercise and pleasure in the brain:

http://www.psychologytoday.com/blog/the-compass-pleasure/201104/exercise-pleasure-and-the-brain

As far as using neuroimaging to measure pathways, I would also look into resting-state fMRI, diffusion tensor imaging, and fcMRI.

For all the rest of your questions, this book seems like a great place to start:

http://www.springer.com/biomed/neuroscience/book/978-1-4614-3292-0

Hope this helped.

Alex