Hi Jen,
Sorry to hear you've been suffering so much! I'm 30, and felt like I had the health of a 78 year-old when I was 28. It becomes difficult to relate to peers who seen to be able to do whatever they want when the "normal" things they do are so not even available options for me.
I've had Lyme, Babesiosis, and Mycoplasmas since age 14. No one tested for them until last fall (15 years later). (Not a bad idea to get checked for mycoplasmas--they are often overlooked). You are fortunate that you got you got your diagnosis when you did. Prior to being tested for Lyme, etc., I received the diagnoses of CFS and fibromyalgia (age 29). I had been tested for arthritis, and they said I didn't have that. Like you, I have observed that CFS and fibromyalgia have a symptom set that is common to a number of different chronic diseases.
However, in my own research, I have also learned that it is possible to set off an iflammation response in the body from deep tissue injury. Having been in several car accidents that caused neck damage in my 20s, I still had trouble believing this when I read it in Shoemaker's book, Desperation Medicine. After attending an Autism conference (I'm a teacher), this inflammation response was discussed in greater detail, and it made sense to me that it is a plausible explanation in some cases. With my lay understanding of this, I can't explain it very well, but I'll try. With tissue injury like I experienced, inflammatory cytokines are released in the body. This triggers a response by the body resulting in fibromyalgia-like symptoms.
I also felt no improvement from the antibiotics and anti-protozoan I was on. I had a lot of damage done to my body since those infections were present for so long. I have some kind of minimal damage going on with just about every organ in my body. This takes time to heal. Some people find success with antibiotics alone, while others do not. I have been on too many antibiotics growing up, so I am planning to use herbals to complete treatment. Lyme produces neurotoxins as a waste product, and for many people, they will continue to have low energy and brain fog until the neurotoxins are flushed out of the body. NutraMedix makes some herbal products that address neurotoxins, and cholestyramine, a prescription drug can also do the job.
Harleyrider's right about the mitochondrial dysfunction--I have that, too. It's indicative that cells are not able to work correctly. I would venture to guess that it's the primary marker of fatigue.
I too, have a lot of chest and bone pain. Even though I was taking TerraMin clay and drinking raw milk for several years in my 20s, I was losing bone. I have bad Candida and leaky gut, which I'm just beginning protocol to address under the supervision of a nutritionist. Because of the malabsorption issues from the leaky gut, I was not able to absorb enough of the minerals. The Candida was thriving on them, instead. The one thing that significantly reduced my bone pain and increased my strength has been using bath minerals. I am able to absorb minerals through the skin. The product I use that has bio-available minerals is called Mother's Dream Come True. The downside is that it's pricey.
The second thing I found that causes me joint pain is when I consume nightshades. Nightshades are white potatoes, tomatoes, all peppers (except black pepper), and eggplant. Nightshades contain solanine, which acts as a natural pesticide for the plants, but causes inflammation in people. I also get burning eyes from them.
Another thing severely lacking in our diet today is chromium 3. It is removed in the refining process of flour and sugar. The body keeps tapping into its chromium stores to digest these foods without replenishing them, and we keep wondering why healthy people have fatigue at age 40. Things I have used to boost my energy include: chromium 3 supplementation with a whole food product like Innate Response or Mega Foods brand. (All other forms and combinations of chromium are toxic).
Foods that are high in antioxidants, especially aronia berries and vegetables. These help the body heal, and the aronia helps it make its own glutathione. D-ribose powder and DHEA supplementation in low doses has also helped me.
Have you had your thyroid and adrenal levels checked? I have Hashimoto's and adrenal fatigue, so I'm on compounded prescription medications for them.
Lastly, other sources of fatigue can include mold and electromagnetic radiation. Mold toxins are neurotoxins, and they can do actual brain damage depending on the type of mold. I encountered this with both an apartment and a basement, and I have some damage from the basement. Molds are often overlooked. I found them in 11 out of 12 aparments in one college town. Mold can be under sinks, in walls, in ductwork, on concrete slab, in carpets, etc. Hardware store tests can identify type but not quantity.
Electromagnetic radiation from antennas, cell towers, cell phones, wifi, and electronic devices causes fatigue in a number of people. I used to live right next to a radio tower, and for the longest time, I could never figure out why I felt so much fatigue and unrest. The trees outside the picture window were beautiful, but I never had peace there. You can search for antennas at: www.antennasearch.com.
Lyme (esp. the co-infection babesiosis) can change your personality. It has changed mine. I used to be outgoing and friendly with everyone, and since then I have become introverted, stressed in social situations, and unsure of what to say. This was a gradual change for me. Very frustrating and isolating. The thing I found the most help with on this front was getting my mercury amalgam fillings removed and detoxing from the mercury under the supervision of my MD. My mood lifted substantially, and some of my foot and jaw (I have TMJ) pain went away.
I hope you find some solutions. Hang in there!