I have a similar problem and have just started with a heel raise. My pelvis is awkward though and tilts the other way, so it's lower on the side with the longer leg!
My right quad is bigger than the left as it's beent aking more weight, and now I'm getting the legs sorted, the left quad is doing more work and is getting knackered as it's not used to it!
In my experience, as you correct one problem, it may kick off others elsewhere. My left quad problem will hopefully resolve as it gets more used to taking more weight, but don't be surprised if you get niggles elsewhere, at least at first. However bad your biomechanics are, your body is at least to some extent used to them, and any change may feel a bit odd.