I developed my own theory that platelets are a component of digestion. Low platelets means poor digestion. Stomach aches and headaches for me felt like it was related to food essentially stagnating in my gut. I think your digestive tract is supposed to be permeable to allow nutrients to be drawn out and carried into your blood and transported throughout your body. There is a syndrome called "leaky gut", I think it's when your gut for whatever reason is worn down and becomes too permeable. Random proteins and what not leak out and are transported throughout your body causing a toxin overload. Think of when you drink alcohol, that's essentially a toxin that permeates your entire body. I used to feel achy and hung over all the time but I wasn't drinking alcohol. I just had the headaches, exhaustion and body aches.
My body felt toxic and my digestive system felt like it was barely working. I did a "food allergy diet" eliminating anything that could be an irritant. I discovered that for me anything with gluten is incredibly difficult to digest. I'm technically not allergic according to a blood test though. I think maybe breads and meat fill you up longer because they are digested slower & they're harder to digest. I used to eat a lot of yogurt to help with the pro-biotics but later went a couple of weeks without dairy and sadly realized I feel better without that too. I still eat meat but go for things easily digestible, fish mostly. A nutritionist had me do a detox where I ate only vegetables, fruit, nuts and seeds. No grains! I did this for a week and felt great. Now I try to keep this diet as an ideal but still will eat rice type grains and meat with attempted moderation. I haven't had the lethargy, headaches or digestive problems since I went down this track. It was slow going but I've progressively felt better and better.
I also had insomnia. I thought I brought this on from relying too heavily for too long on caffeine to combat the exhaustion somehow throwing off my sleep wake cycle. I started taking a combination of supplements for insomnia. 5-HTP, lifetime liquid cal/mag, vitamin D all before bed. This worked for me. I believe I read somewhere that melatonin is not good for people with auto-immune issues and it made me feel exceptionally exhausted so I didn't take that.
The 5-HTP however is a precursor to tryptophan, the ingredient in Turkey that makes you sleepy which is also a building block for serotonin, which is then also a building block for melatonin. I tolerated this supplement very well. I've since read that platelets carry the majority of your bodies serotonin and I wonder if low platelet counts can contribute to the lethargy and bad moods that come with my low platelet counts if that means my body has less circulating serotonin. I don't really know but I think this helped with my moods too.
headaches.about.com/cs/alternative/a/5htp.htm
Everyone reacts differently with supplements so I would proceed with caution when using natural supplements but modifying the diet, to me seems like a must do, or at least try, if you have been diagnosed with an auto-immune disease.