Nightshades

So... Someone read the previous post, which included the recipe for hearty vegetable soup, and asked me to clarify the 'nightshades' remark. Here goes: I have been having some new food issues (such as really sore joints and generally just not feeling all that well for several months) and my doctor told me to try a new elimination diet. I went grain-free (no corn, rice, or quinoa) and dairy-free for a month to try to sort things out. That seemed to help, but I had been having some issues with joint pain and still wasn't feeling completely spectacular. She checked me for some autoimmune things that could contribute to joint issues and didn't those were responsible. I was then told that she has recommended that some of her patients avoid nightshades to see if that helps. What are nightshades? It turns out that potatoes, eggplant, sweet peppers, and tomatoes are all nightshades that I was consuming on a very regular basis. I cut most of these out and that actually seemed to make a big difference. My body isn't aching as much after running so it seems that avoiding these has been helping, although I do love french fries (especially with gf beer!) but really only eat them occasionally.
I worry about completely cutting certain foods out, though. Some of these, such as red peppers and tomatoes, can be very good sources of vitamin C and tomatoes are an excellent source of lycopene. I think that I may try to eat these only occasionally. As far as potatoes go, I have been successful at switching out potatoes for yams, which seem to offer more nutrients than their potato counterpart while also being a good source of complex carbohydrates.

I have tried to faithfully capture the advice of my physician, and I invite any criticism, suggestions and comments you may have.