Do 3 sets of pull-up, push-up, inverted row, dips in circuits with 90 sec rest between sets. If you cannot do it in circuits, try resting 30 sec between exercises and 2 min rest between sets. These are all body-weight exercises and very efficient way of training. you will be able to finish it in 30 mins. Do it in your every training, your body will get used to it overtime.

visit /r/bodyweightfitness to learn proper forms. pull-up, push-up, inverted rows have their own progressions (seriously they are way harder). for dips, you can add weight.

If you have more time life, you can add handstands which works nice for your shoulder. you can progress it further to handstand push-ups.

Since you are running a lot, don't include any leg exercises such as squat etc. If you want bigger legs, cut your running time and do weighted squats.

Don't do any isolated exercises such as bicep curl etc. pull-up, push-up, inverted row, dips will do good job of your upper body.

If you really want to add weighted exercises. add whole body exercises such as deadlift or powerclean. they will give you explosive strength