The thing is, RA is not going away when one stops activities, this is not one of the characteristics of this auto-immune disease.
Another thing, RA doesn't affect our backs, thank God for this at least.
But OA may. At age 25 and older our spinal changes start, age related. Since you are 41 and a runner, your body may need some changes too regarding activities.
I used to exercise 5 days a week, really hard and serious, but one thing I wasn't able to do anymore is running outside, this was stopped earlier than my gym activities. Also due to pain and changes of my body.
Earlier menopause of course affects your thyroid function, I had my partial hysterectomy at age 35 and body did I feel it!! Here is your cold hands.
About your knot; sometimes we get them on top of our feet or on top of wrists/hands, either from tight shoes or carrying something heavy on our wrists and hands. Painful, but it goes away in time if not aggravated anymore.
RA is a lot more than just leg pain or foot pain. Possible you get your pains from thyroid dysfunction and body changes or just age related OA. If this concerns you, please see a specialist, but personally I wouldn't worry much about having RA.
I am not a doctor of course, but this is just my 2 cents.
All the best to you dear