Lower back pain is typically caused by tight hamstrings. From a fitting POV, increasing the drop between your saddle and bar could contribute to this pain. While 3.5cm isn't terribly aggressive for a 20-something racer, it's unusual for a recreational rider. You could add a stem with a greater degree of rise to ease the lower back issue.

How significant is your leg length discrepency? Do you know if if it's dynamic/functional (ie caused by variable flexibility in your hip joints) or if it's a bone length discrepency? If bone length, tibia or femur? The answer to these questions will determine if you need correction and which method will work best for you. A discrepency of 1-2cm doesn't necessarily need to be corrected -- your body will compensate for it. More than 2cm is considered significant and should be corrected. The most common lld is dynamic or femur, both which are corrected by cleat positioning (you fit your saddle height for the shorter leg and then move the cleat on the longer leg back to increase your extension). Less common is tibia, corrected by shims. Variable length cranks are extremely unusual as correction for only the most significant discrepencies.

Hope this helps!