Do you do soft-tissue work on that side? Like foam roller or tennis ball rolling? Quads, ITB, piriformis? My first thought is that because of the original right knee problem, you have a tight ITB, rec femoris, piriformis. The piriformis can effect the sciatic nerve and cause pain all down the right leg there, perhaps the knee in this case. Tight thigh tissues (ITB, hip flexor) can cause the knee pain as well.
And if you have a tight piriformis and weak glute medius (perhaps from underuse while favoring the injured leg), then your QL (quadratus lumborum) on the right side may try to pick up the "slack" when that one side is overloaded. Hence, the lower back pain.
These are all just thoughts and suggestions to consider, not a true analysis.
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