Sorry you’re struggling with knee pain-that’s really frustrating. Your increased sitting no doubt plays a role, but my first thought when reading your post is that there are probably some movement patterns with running (especially downhill) that are causing an imbalance. Hip strength and extension are super important for stabilizing the knee, and while it sounds like you did that with specific exercises, transferring that to the way you run may be the next step. I wrote an article on downhill running here: https://uphillathlete.com/downhill-running-technique/
I would focus more time on the posterior chain muscles for strengthening rather than the quads, as sitting shortens the hip flexors and quads, so that it’s more challenging to engage the posterior ones. Some mobility for the front of your hips may also really help. Low lunges (passive, with your back knee on the floor) help open up the front of the hip and the couch stretch (google this one) is terrible/great for stretching the quads. Foam rolling is also helpful for increasing mobility in the hips: https://uphillathlete.com/foam-rolling-why-how/
With more sitting, your glute muscles may have gone on vacation, so doing exercises like bridges help wake them up and bring them back on board.