Yes, many people can experience these kinds of symptoms when making diet and lifestyle changes. The good news is that these are often a sign that you have the most to gain out of the program. Often people who go from eating a poor diet to one that is clean and nutrient rich or no exercise to a program like this will experience fluctuations in mood, energy, and may even experience flu-like symptoms like headaches, body aches, and so on.
For most people these symptoms disappear after about three days. For some they may last as many as 7-14 days. If your symptoms last longer than that, you should review the AIM protocol and start figuring out whether or not you should make alterations in your diet ot help you balance your SHMEC.