You may have trouble with running at this stage of progress. cycling, elliptical and scwhinn airdyne may be a better choice for cardio, then as your doctor permits you can start a walk/jog program with recovery days.
Strength training for your lower body should be a main concern, again after your doctor and PT give the ok. If they give you restrictions on training, do not go against their recommendations. Body weight exercises (squats, single leg squats, step ups, calf raises, sport cord exercises -lateral jumps, single leg partial squats, etc.) are a good place to start. Then with help of a strength specialist, you can work into leg press, leg curl, weighted calf raises etc.
You will need to regain the muscle you have lost, this will require more protein in your diet. Have the required amount of protein with every meal and you may need additional calories daily to build.
RDP