You do not need to worry about these pains, as long as they are not radiating towards your feet. Most probably this is due to your recent running of hills. Take plenty of fluids. Use warm compresses in the morning and ice at night. This will help relaxing the muscles.
Keep well hydrated while you are exercising and use a fluid which replaces body salts. sometimes muscles can cramp due the lack of electrolytes in the body. I do not suggest that you take complete bed rest
specially with military training coming up. I would just suggest that you take it easy for a week for your body to recover, and increase the intensity gradually. And take special care of your diet.
Take care of yourself.