Have you tried cutting out the tomatoes from her diet completely to see if that makes a difference to her poo? Are there any identifiable chunks of food in it (gross, i know) to help you identify what foods might be the triggers? (eg if you notice blueberries, you know that if she had beef, potatoes, peas, and blueberries at supper time that one of those might be the trigger)
I have heard of toddler's diarrhea though and it can last for months
Have you tried using food from the BRAT diet (bananas, rice, applesauce, toast) to see if that bulks up her poo at all?