Though I use software applications to monitor and track some personal metrics, I have never found an application which is easily usable for long term recording of diet and symptoms. I have used similar diaries to help alleviate migraines and insomnia by detecting and avoiding their causes. The process can take months or even years, but will usually produce results more quickly if done with the consultation of a trained dietician or other specialist.
I always recommend to friends that restriction diets be embarked upon with caution. Restricting the diet may reduce valuable caloric input, which itself is a health risk. Once during a mysterious and unintentional bout of weight loss, my doctor told me to go out and buy all the junk food I could carry home. Obviously she made no claims about the junk food's curative properties, but avoiding further weight loss was more important than avoiding salt, sugar, and fat.
Remember, everybody poops. Even if it's in their pants.