Given what you've described, I would recommend a regular yoga or pilates practice with an instructor(s) who really understands anatomy. Stretching will presumably help with some of your flexibility issues, but I don't think it will help you strengthen your core and/or deal with your muscular imbalances in the way that a regular (and by regular, I mean 2-3 classes a week) practice will. I started yoga at about the same time I started riding and it's worked wonders for my back, abs, hamstrings and hips (although they remain my bugaboo). It's a very good counterbalance to cycling.