Adjusting pedal / crank / other components to account for different leg sizes I added a heal lift (~1 cm) for running to my right shoe after learning my right leg was slightly shorter than my left. Doing so alleviated any pain I was experiencing in my right knee.

However, I'm now regularly commuting, and the added miles seem to be adding up, as I'm experiencing pain in my right knee that seems to be due to the issue corrected by a heal lift. 

Does anyone have any suggestions for how to somehow make an adjustment via pedal / crank / other components such as shoes to account for slightly different leg sizes?
I've done the same thing in the past, heel shims, cleat wedges, pedal washers, insoles, etc. 

The one thing I can say is that it's a slippery slope once you start fiddling with these things. 

One small adjustment effects all the others and it's very difficult and time consuming to get it right, which you probably never will without 3rd party perspective and expertise. No to mention there are a bunch of other things that can be causing your pain besides leg length difference; fore/aft foot tilt, knee alignment, saddle position, etc. 

The real solution is to get a professional bike fitting.