Sounds like a case of protein deficiency due to incorrect diet - incorrect diet will stress your digestive organs, and can result in nutrition deficiencis - this can cause depletion of enzymes and stomach acid which is essential to proper digestion (specially protein). If you cant digest protein (break down into amino acids) then you will be AA deficient - AAs are essential for every tissue - the digestive walls is made of these so leaky gut can result with AA deficiency - AAs are essential for collagen production which are present in high levels in joints and skin so Arthritis fibromalgia, skin disorders can begin ocurring with protein deficiency (AA deficiency).
You need AA to manufacture all enzymes and hormones so a long term AA deficiency will result in hormonal problems (anxiety, sleep disorders etc). You also need AAs to detoxify the liver on a daily basis so toxins can accumulate in the system. Also since the digestion is brought to halt, the food you are eating may not be digested properly which means opportunistic pathogens will thrive in your gut and create dysbiosis. They will ferment and putrefy the food you dont eat, creating more toxins and making you bloated. Also food allergies appear because the gut all is now permeable, allowing large food particles to pass through and create havoc.
All because the standard diet is loaded with processed dead food that is heavy in protein (which depletes your limited sources of enzymes etc) but most importantly eaten at the wrong times and prepared the wrong way.
Boost your digestion with digestive enzymes, betain HCl if needed , but more importantly take a good source of aminoacids (FREE FORM so that is readily absorbable) - also a good source of hydrolized collagen will provide plenty of aa's.
If you tried to eliminate meat from your diet and got sicker (like i did) then its possible that you are parasympathetic metabolic type and require larger amounts of protein. You can do this but make sure you supply with digestive enzymes and boost you HCl levels to digest it properly.
Also good source of EFAs did wonders for me (I take 4:1 omega 6:3 ratio) and carnitine to increase their uptake. Sodium (Sea salt) is absolutely critical to make digestive juices (look into the Water Cure ).
Also you may need to double check you ca/mg ratios to eliminate muscle tensions. (personally I need a higher level of Ca than normal).
Study ayurveda body typing, Dr Price and Dr Kelley viewpoints - I've been in a similar situation and now am slowly pulling away from it. http://www.supernutrient.com/fibromyalgia.cfm?pageInfo_ID=41