I am so happy that practicing at Sunstone is giving you so many wonderful benefits. You will continue to see more over time.
Presuming the pain is in the leg that is kicking out.... Noticing the differences from on side of the body as opposed to the other are a great sign that you are gaining body awareness. This can occur in other postures as well. For example, in cow face, I find I can grip when my right arm is on top, but not quite when my left arm is on top. My first reccomendation is to not force a symmetry on both sides. Instead go only as far as your weaker side. This will help balance your body instead of creating a larger gap between both legs. Never force anything. Your body will open over time so enjoy the journey.
Presuming the pain is in the standing leg... Engage the muscles in your calf, thigh and gluteus strong, then straighten as much as you can without losing that strength. This will help protect your knee and hamstring.
Regarding your shoulder modifications. Ask your teachers what the best modifications are to give you the greatest benefit in each posture. We LOVE talking about yoga