I have been working out for about 11 years (I am 37) but the past five years have been harder Crossfit Style workouts. I was the leanest and strongest that I have ever been and LOVED them....but a naggig back pain caused me to stop about six weeks ago from those workouts. Since then I have been doing cardio stuff (biking, swimming) and trying to get some weight classses in at the gym but I am gaining weight, feeling sore and sluggish all the time and not sleeping as well. I am eating really clean right now to combat the drop in exercise. Could I have worked out my body so much in the past 11 years that now that I stopped it just doesn't want to do anything else? I am worried that I am still young and have my whole life ahead of me but can't find anything that I can do right now. Any thoughts?
Yes it can.
Many professional athletes have life-long injuries from their training.
Find a good physical therapist who can help you - it sounds like your having some im-balances that can be solved.
First and foremost, if you haven't already, go and see a professional about your back. Even minor back injury is very serious and can cause further damage if it's not properly dealt with. You should really get advice from an MD or physical therapist to prevent any further injury. Even if you have to really baby your spine, there's a lot you can still do in terms of strength and cardio without aggravating it.
What sorts of cardio are you doing? If you were in crossfit before the back pain, you might enjoy Tabata or other forms of HIIT. More isolated weight training is probably advisable, avoiding those big compound movements (squats, deadlifts, etc). Think about leg presses on a machine rather than squats and keep that back straight when using free weights in any position.
I'm sure you'll be able to figure out a satisfactory routine with time! Good luck!
EDIT: You mentioned you are "eating clean" and still gaining weight. Can I see your macro breakdown, calorie count, and meal timing? A lot of people swear by the IIFYM approach (if it fits your macros), but I've come to really believe in the intermittent fasting protocol. There are several approaches to IF but regardless of which one you choose you will get some major hormonal benefits. There's even some research into increased longevity and cancer prevention using a fasting protocol. Here's a Scientific American summary of the research which has some of the potential downsides listed as well. Leangains has been great for me while training, though I keep the carbs more limited than Martin Berkhan suggests. It's really helped my body composition without detracting from my training. Some people respond negatively though, so keep an eye on yourself and if you don't feel awesome after a week or two, try something else. There's a bit of a transition period, but after that my energy levels in the morning actually increased significantly and I now train exclusively in a fasted state. Your mileage may vary!