Sometimes ammonia odor is caused by what you eat. Food do impact on your breathing odor, and other times, this can be associated with some kind of kidney diseases. We don't know what exactly it is, but I stronly suggest you to make an appointment with your doctor and run some tests. You can't be too careful. Hope everything's fine.
You have to increase your fat and carbs and protein. Your body is breaking down all the protein you get too fast, but the fats and carbs are broken down first, so this means you probably need more of all three if you're working out.
Have you been eating asparagus, that happens sometimes.