You know I hear what you are saying a lot. It's interesting to me how many of us get into this rut your having filled with emotional baggage, lack of motivation, and generally a bad attitude towards fixing the health issues. Your issue strikes a lot of chords with me because my problems parallel what you were saying. School, injury, family things etc. I wish that I had the right words that would sink in that makes an individual reverse all that negative process. Heck if I could do that I would be even further along myself. Unfortunately there just isn't a black and white statement that fixes us. I do believe that every one of us has the ability to dig deep and fight it and really fight back hard. What do you need to do that? I'm not sure.
Personally I've never been a sports oriented guy with a huge background or anything like that but I've always been fascinated with the process of becoming fit and the physiology behind it. It would be interesting for someone to study the psychology of sport in a way that would be helpful for regular "joe's" like us versus elite athletes. Hell if I could figure that out I'd be so rich I could buy an island heh.
Its hard to tell folks that their lifestyle habits are causing or going to cause significant health problems in a way that doesn't further worsen their negativity or cause them to just ignore it altogether. Believe me I've spent 20 years in the medical field trying to do just that. The nice thing is that you are concerned about your welfare which is the first step. So, how do you continue taking the right steps?
First off we need to understand that our bodies are just not meant to be still except for sleeping. Our physiology doesn't allow the deviations that current society is trending towards. Fight or flight response is heard so much that I think most folks tend to just hear it said but don't really listen. As a matter of fact your statements indicate that you are having this reaction now. Your body wants you to react to this and your mind is confused about how to respond. This all sits on a very deep subconscious level and conscious level but the subconscious is throwing a fit. Sounds kinda crazy but think about it. How many times in the past year have you had a disagreement, worried over a job issue, family, spouse, gotten into an argument, worried about your health etc.? These are all fight or flight reactions even if only on a minor level. How did you respond to them? I'm guessing you didn't get up and punch someone in the face or sprint down the street right before you walked down the aisle? Common sense dictates those as abnormal reactions but fight or flight doesn't because that is how the body wants to respond. You see we live inside this vessel called the human body that is based purely on being a survival mechanism. Not much call for those kinds of things today. The mind gets confused and lazy, and the body suffers eventually.
There is a fix for these things and that is simply exercise. As you do it the stress reduces and the body responds by becoming more capable to handle the difficulties you throw at it. But you also have to make it a bit harder and more challenging otherwise the body is essentially working but not responding to all those flight or fight issues you handled during the day. The thing we have to remember is that the stress never goes away, its just that your mind and body develop in ways that handles it better.
You also have to figure out how to live with your injury. You still have the capability to be fit and healthy even while hurt. But you need to do your research and study the movements and know what makes it hurt versus what doesn't and if it does hurt why? Whole books have been written on this subject about the right way to do this and what exercise is best for <insert injury here>. Personally I believe any and all body weight exercises are doable for the individual but you need to know the proper body mechanics and you don't need to do anything that aggravates it. For example, after my shoulder injury I wanted to do pullups and I had pain everytime I got on a bar. I learned over time the right way and the wrong way for me to be on the bar. Now I'm pain free when I do them but if I get on a bar and hang like I did before it hurts. And if I were to continue that way I end up with pain that doesn't go away without medications and rest, icing, etc.
As you decide what to do and how to live your life remember that this journey takes a lifetime, takes dedication, and starts with the first step. Which you have taken. Continue your journey, think about what you want to accomplish, find a way to make that happen, take small steps to get there, and soon you will be in better shape than you thought possible and you will likely find that your thought process are better suited to this as well.