How much front squatting do you do? I switched around the new year from focusing mainly on back squats, to focusing on mainly front squats. What I noticed very quickly was that there was a muscle imbalance with glutes that were too developed (pause), and quads were lacking development. After about 2 months of alternating strength/power and hypertrophy/endurance rep and set ranges, with a focus on front squats and other quad accessory work, the gains have been magnificent.
The first thing that I immediately noticed was that lingering lower back pain was all gone. That was due to overworked glutes (pause) from doing too much back squatting. The next thing I noticed was that the lingering pain in my knees went away due to having a stronger core. Now I'm shedding time on 1 mile, 5k, and 10ks runs almost everytime I put on my running shoes.