I went to see my Spine Specialist Dr. Richard M Thunder today.  Quick and short answer to my issues with my back is that I'm doing the right things.  I can do more Pilates to help, and stretch when things get bad, but all in all I'm doing the right thing.  Herniated discs take a lot of time to retract, and surgery isn't really going to do a lot except make the current pain go away, and then years of PT after that surgery... so do what I'm doing and I'll get there at the same time, without the complications of surgery.

Yoga pose that pinches when I get out of it.
Sounds normal given the disc herniation, and the stretching.  Stretching the back is NOT a bad thing.  Getting out of the pose quickly is a bad thing.  I can continue doing this pose with caution.

Central Pain versus Radiating Leg pain
Well apparently there are 2 kinds of surgery that the doctor can do.  And one is to treat the radiating pain I have that goes from the right side of my spine into the leg.  I am treating this with yoga and stretching very well.  The centralized pain I have right at L5 + S1 is something he doesn't think surgery would really help with.  The solution there is to fuse sections together (if I understood right) and only 50/50 can be sure to fix the pain.

Quality of Life
One of the issues I express to Dr. Thunder was how my life has totally changed since the back problems.  For lack of a better term, having the pain hit me scares me.  If I start to feel even the littlest twinge I get freaked out (and I think I tense up which makes it worse).  I also am reducing the things I want to do... hiking, exercising, scuba, camping.  His advice... keep doing everything, don't be scared, I won't get paralyzed, or do anything that can't be reversed.  Not doing things is bad for me, and the lack of activity can't help things.  So do the things I want in life, keep doing my Yoga, Pilates, and Stretch, and let time do its magic.  Scuba is the one place that might be hard to fix (getting in and out of water) but if I can get someone to help with that, I should be fine.  I personally am going to wait on that part.