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I went ahead and spoke to a close friend and he said I wasn't getting nearly enough fat in my diet, and my chiropractor said to increase oils as well, he suggested fish. I immediately went home and hand a small handful of macadamia nuts and an avacado salad, and flax, hemp, coconut and udo's oils (since I really didnt want to compromise my new-found veganism with fish oil). I've kept up this regimen for a few days and am happy to report that I don't have the severe ache anymore, and actually completely a 65 minute run without any abnormal pain whatsoever, just reasonable muscle fatigue. The explanations I've been getting is that because of a lack of enough fat for my high activity life, my body was cannibalizing my muscle tissue as a form of fuel. It makes complete sense, and I've also upped the amount of protein sources in my diet, as I was unaware that I wasn't getting complete protein unless I combined two or more rice/nut/grain proteins in one. So far good results, we'll see how long this lasts or if any further amendments are needed.
If you're eating soy (as you said you were increasing protein on your vegan diet), this will give you achy joints. One month I bought a box of soy cubes as I was going to put them in my stir-fry and I did. However, I was crying for a good two weeks. I was in agony to a point where I thought I needed to be put out of my misery. Definitely steer clear of soy anything and don't forget to look at your supplement bottles as they may contain soy too. I won't tell you what happened to me after 12 years of eating soy and drinking coffee. Soy blocks vitamin and mineral absorption and coffee washes it right out of your body. So you can imagine I went through a lot with my body. 50lbs overweight and malnourished not to mention severe alopecia and body pains and aches and...well, I could go on. After stopping it for a good 6 months with 3 months of my body detoxing from soy and I stopped coffee 2 months ago, at least my hair is growing back and no more severe IBS. :D