It takes a while for all the support muscles to strengthen. Once the body pain stops or at least is manageable the best way to improve your heart’s ability to keep up on the run is to interval train. It sucks but it’s worth it to pick up speed and stamina.

Oh yeah; do a good stretch before and after the bulk of your run. Focus on the areas that are most sore after you’re done. I have plantar fasciitis and tight hips so I do a ton of hip and calf stretches once I’m warmed up, and when I’m cooling down.