Update: I've been limiting myself to 5k runs and High Intensity Interval Training (HIIT) sprint routines so I limit muscle atrophy. I've noticed that my runs are much easier and painless now that I have switched from over-engineered shoes to wetshoes (removed the soles and the ripped out the padding). I've also noticed a general increase in strength in my feet. Before actually getting shoes, I did a lot of 5-8k runs on various terrains, including cobblestone, which actually felt good after a while. Once I return to school in two months, I plan on beginning some weightlifting, including deadlifts, benchpress, squats, cleans, pull-ups, etc.
I've also noticed that through HIIT I've lost quite a bit of fat. Sadly I'm not that big of a guy, so I'm definitely looking into some foods that increase my caloric intake (oatmeal, multigrain bread) or gainer shakes.