I was your age (~44, so 10 years younger than I am now) and training for my ~5th marathon. Started to get knee pain DEEP in the knee if I did a full bend (like sitting on your knees). I have good knees, always have, but have also had various injuries/pains associated with endurance running. I casually saw a PT and unbelievably her response was just that after a certain age, “don’t do that anymore. Don’t bend your knee all the way.” But someone else overheard this and took me aside and told me the exercises to do. The point is your joints are supported by complex chains of muscle, fascia, tendons. A knee, ankle or foot problem could be caused by your hip, heck it can be caused by your neck or shoulder!
Of course, DO NOT run or push through this kind of pain. I too have made this mistake, and paid for it in YEARS of not being pain-free and developing bursitis.
One of the excellent points in Born to Walk (not a flawless book, but I love this point) is that the injury rate for amateur running is WAY too high. And he says, the number of people getting stress fractures is ridiculous. (Thankfully have never had that.) A stress fracture, according to him, is something that starts as a small muscle knot that you IGNORE for months. He says your bones are so strong, that for them to begin to develop hairline cracks means you ignored something wrong for WAY too long.
Also the newest science is finding that the cure for osteoarthritis (not rheumatoid) is MOVEMENT, explosive in fact. You create the necessary lubrication by using the joint.
Kneesovertoes guy on YouTube is a treasure for this kind of info. He’s in his 30s, and has his almost 70 mother running sooo fluidly and fast thanks to his exercises.
Final point, I personally think that we grow into our body our whole life. For some reason (emotional?) I had bad back trouble from teenager to early 40s! I haven’t had back or hip trouble now for 10 years. Every problem our body gives us is something we have the opportunity to try to solve. Not saying it’s easy, but achey joints is telling you something is out of whack. I have ZERO aches, I’m closing on a decade of menopause, I feel younger and fresher than ever. The human body is not meant to decay due to disuse, but our extreme comfort/EXTREME sedentary life and extreme overstimulation mentally (which causes bad stress*) is causing fast aging in some people.
*bad as opposed to good stress, since stress is necessary for growth