Adjusting pedal / crank / other components to account for 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.