hey, just skimming through here, the running is really good, but it's bad on the joints after awhile, as you may have noticed. Especially if you're doing it outside and not on the treadmill.
I recommend changing it up abit, and maybe go on an exercise bike or even an elliptical a couple days a week. Cardio is important to weight loss, no doubt, but it needs rest too.
I used to do the body part a day thing, and it did give me results, but i think a better approach for what you're aiming for might be working out a whole group a day. For example: upper body day 1, lower body day 2, and back on day 3. Having a friend will really help your motivation, it's great to have them. After about 3 weeks of working out, that pain you feel the next day will pretty much not happen anymore. You're just shocking your system so much right now, but it will adapt.
If you do too much cardio, your body WILL crave, and crave and crave, more food. You don't need to starve yourself to get good results. But your calorie consumption estimates is a really good baseline to go by. If you're eating the right things (protiens, not too much carbs, good fats) you might even have to force yourself to eat all the calories in the day. Try to eliminate sugars (minus fruits) and soft drinks (including diet sodas). Your appetite will thank you.
If you can't get to the gym very often, I also suggest getting a chin up bar, and even resistance bands. I use 3 bands on one set of handles, and it's almost as good as using free weights. You can experiment with them too, so when you get to the gym, you can do similar exercises with free weights.
Good luck, stay on it, and you should have no problems reaching your goals