Gosh - it all sounds so familiar - I was diagnosed with a herniated disc after several misdiagnoses and after 2 years of having pain down my leg. I have been in rehab for the last 6 months and finally (and v v slowly) I am getting back to normality. And by normality I do NOT mean 15 hour training weeks, which was normal for me before, but to being able to sleep and turn in my sleep and sit down and not have to kneel behind my office.
The best thing you can dom, IMHO is the following:
1.Find a good physician, whom you trust 100%. Don't be afraid to search. Of course it does not necessarily mean someone who tells you "you are fine, go run". But someone who seems to know their stuff and is sympathetic to the type of lifestyle you would like to lead. My doctor happens to be a mountain-marathoner and IM himself and realised from the first moment that being physical is part of who I am. He has given me hope when I have been down and has helped me to believe that I will be able to get back to (some level of) fitness again.
2. Do your research. Get an anatomy book. Learn as much as you can about what's happening to your body. Have someone explain your MRI's and X-rays thoroughly.
3. Keep a diary. It really helps you see the patterns. I had been told that swimming would be fine, but it was the case that I was getting pain after every swim. I tried to attribute it to all sorts of things, but ultimately my diary made it obvious. I can now go back to swimming and I am building up... currently at 1200 meters, NP (no pain...)
4. Know your body and listen to it! Accept your (current) limitations and work within them, pushing the limits v slowly. For most athletes this is soooo hard, but you have to listen to the pain!
5. Enjoy and relish the pain free days - they will come and they will get more frequent - I used to have one a month I am now around 25 per month and hoping to get better!
6. Do Pilates - it was in fact the one single thing that made me get stronger and back to fitness. Do a little every day and see your body get stronger.
All the best with your recovery.