Great to hear you are increasing your knowledge about the body.
Good that you are seeing some improvements in range of motion.

Are your knees coming forward first?
If your knees are coming forward first then your load ordering is off. In this case your knees are loading more because they are being loaded first.

The other knee may have started to hurt from the increased volume of lunges and squats.
Do both knees currently have pain when squatting?
New range can be sloppy range at first.
You can have more discomfort with your improved range of motion since you are in new positions. Your knee and/or are working differently than they have in the past. You may be using muscles differently as well.
The change in range of motion can bring other restrictions to light.
Thursday, August 17th, 2017 – Calcaneus Check
Free Your Heel, Free Your Mind
Pro Episode # 44: The Last 25% of Your Ankle Restriction (Snatches and Pistols here we come!)