Good post. I've experienced something similar that you are describing. What I concluded, It happens when I am unprepared to long distance run. For example, after 2 weeks of pause, I got back straight with 11km training, that made me feel something was happening around the knee (under, on the outer side pain), hip (very mild pain), but also on my toe (cuboid bone). It wasn't much painful, but when one starts to hurt, it is like a chain reaction.
And about the hip, sometimes after long-run day, I feel popping sound somewhere in the hip but is also somehow connected with knee, depending on the move I make. I feel that's connected, but I cannot specify where exactly, and what exactly makes the sound. It feels like at the same time in the hip and knee..
I am very cautious about that, and, luckily, the pain is so mild and is fading. Only the sound is annoying, as I don't know precisely what makes it. My physiotherapist told me (while I had another injury) the popping sound is only air between tendons.