Joint pain is a common symptom of Lyme and co-infections but Lyme arthritis rarely causes the type of joint destruction characteristic of RA. Are your joints red in appearance and hot to the touch? To my understanding RA also causes those symptoms, while Lyme arthritis typically does not. (Hedging myself with the word "typically" since I'm not a medical expert and their are always exceptions to rules.)
I did experience some joint damage due to my illness, noted by a rheumatologist during a physical exam. She noted my knuckles were "filling in" somewhat and also some hard nodules on my hands and feet that developed. She was concerned about lupus and RA, but my tests were negative on separate blood draws.
My joint pain has diminished with antibiotic treatment, but was always worst in my hands and feet. I do still experience morning stiffness, a symptom that can span RA and Lyme, but it is less severe than it was. My inflammation markers (SED rate, c-reactive protein) are consistently high on blood draws, consistent with these lingering issues.
It is definitely a good idea to keep an eye on your Vit. D levels. I know there are some conflicting theories out there on whether or not, or to what extent, Vit. D should be supplemented, so I'd discuss it with your doctor. Some diseases, including Lyme, are theorized to deplete Vit. D levels, and there are also links between Vit. D. And autoimmunity. I'm not an expert in any of these theories, I just know they are out there and am mentioning them in case anyone wants to look into them further.
My Vit D levels at times were extremely low, and supplementing did help me feel better. (Not with joint pain specifically, but with other weird issues like my legs feeling unnaturally heavy.)
There are a million causes for foot pain. It's possible that if you have any pre-existing foot problems, the inflammation from the Lyme could be aggravating it. For example, before I got very sick I developed a bunion. It would hurt from time to time, but after my Lyme got bad the pain from my bunion became much more severe.
Hope you feel better soon and that the RA tests are negative.
Have the both of you had your vitamin D levels checked?
I have pain in all my joints and one time had a pain in my one toe which made it feel like it was broken.I could barely walk. Now my joints just ache and throb and this has remained fairly consistent. I am not sure about the connection between lyme and RA. I know RA causes joint destruction. It's possible it's just lyme arthritis.