Sounds like you have a set of complex issues feeding off each other. Mobility (K Starrett!) is going to be a big piece of solving that puzzle, as is single leg work for your weak leg, glute activation work for what is most likely sleepy/nonworking glutes with your depth problem, and a decision to sacrifice weight for a while to nail form. Goblet squats will help to nail down form, but won't do everything regarding fixing your problems with mobility and feeling only one leg working.
You'll need a video posted--make sure when you post the video you mention that you are squatting for bodybuilding purposes, as powerlifters will otherwise assume competitive powerlifting goals and respond accordingly.