One thing I learned from logging my food is that if you eat the same few things all the time it makes a massive difference if your information is incorrect when you log. Basically if you eat something once and it's actually 300 calories instead of the 500 you think it is, it's no big deal. But it's a really big deal if you eat it 4 times a day.
Just a thought.
Although it wouldn't account for all of your problems, you may also be having some nutritional issues because of your limited diet. Do you do a multi-vitamin?
Current PRs at 242- 495, 335, 545, 1375