There are various muscle aches that will happen and that same co-worker who shared his insights on getting the most out of a run also had some interesting things to say about what kind of pain to just work through and those to pay attention to and his answer was elegantly simple, if it is a sharp pain that's debilitating than you should stop. He also asked what shoes I wear for running and when I said New Balance, he warned that if I experience sharp pain where my pelvis and femur meet (any MDs, what the f is that joint called?) that I should consider changing shoes as New Balances favor those with bad arches and mine are fine. Because of how New Balances are shaped, it forces an inward cant which may lead to sharp pain at the above mentioned joint was the explanation. This he mentioned is not true to all New Balances, just those with a ton of cushioning and he suggested the minimalist style running shoes such as the Nike Free series maybe the way to go (and also mentioned that likely is cheaper too!). So far I have been fortunate that I have not felt these ill effects but have been paying close attention to it on each run.
As for the Get Running app I mentioned in my first running post, it's awesome. The app tracks the days you run and the running routine is already mapped out by each week, it is exactly what I wanted; a way to track my progress and improve upon it. Assuming that I stick with this, I think that the next evolution would be an app and device that would track my runs, perhaps the Nike+ line of gear, something to look forward to for when the nine week running program is done.