I say this based solely on my experiences with my own muscle imbalances, but most of the work that I needed to do--at least initially--was off the bike. I'd start with a reputable physical therapist. After a detailed assessment, he/she will probably give you some detailed exercises designed to balance the strength of your left and right sides, as well as your inner and outer legs. Short of some other biomechical problem, like a leg length discrepency, I'd try to work on developing a smooth and even spin. The best way to do that, arguably, is with a good set of rollers.