Just got back from my bike fit at Pedal Precision in Manchester Velodrome.
Spent a while discussing what issues I've had, mostly my right foot not sitting flat on the pedals, a few back ache issues but that was pretty much it. He then went on to explore the extents of movement of my legs, how I walk and how my feet-ankles-knees-hips-back interact in the "chain" as it were. Then spent the next hour on the turbo and made quite a few adjustments to my setup.
He raised the saddle a bit and moved it forwards, lowered the bars and tilted them a bit back towards me. My main problems were that my core is not properly supporting my body and my glutes were highly imbalanced which was causing all the issues on my right hand side. My left bumcheek (for want of a better term) stays pretty still whilst cycling and my left leg in turn pistons quite well and smoothly. My right however moves up and down because there is little strength in the muscles that bind the pelvis to the spines which was causing this extreme "wobbling" of my right cheek (so to speak). He made various cleat tweaks, removed my insoles that had padding on them, made his own with some tape, along with the other bike changes and has given me a list of exercises that I can do to help redress this imbalance.
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I have similar imbalance. With me its the left glute area. I am trying to strengthen it with bridges, one legged squats, lunges, clams and some resistance band work. It doesn't hurt on the bike but does seem to create a bit of medial knee ligament strain. Its all interconnected!!!