I feel your pain and commend you on taking responsibility for your own health and not relying on dermatologists and doctors. I took Accutane 3x many years ago when I was in my 20's and didn't know better and it never worked.
What I have found to work the most for clearing up my skin from the inside out is doing a colon/bowel, liver, kidney detox/cleanse. It's about 1 month but it completely clears everything out. During this time you do have a limited diet of mostly fruits, vegetables and juicing. But yes, when you start adding the foods back in after a couple of months I do start breaking out again.
Much like you I suffer from much worse Acne in the winter time and I believe that is from lower levels of sun exposure meaning less Vitamin D intake. I live in sunny southern California so spend a lot more time in the sun in spring/summer which clears up my skin. I do now supplement with 5000 mg Vit. D supplements in the winter, Solgar is a good natural product. This has helped a bit. I also started using the new Proactiv and it actually works.
Regarding being very active and running, I too used to be more active and found the more I sweat, the more I break out, so I've switched to more low impact activities like yoga and if I am very active I shower right away as soon as I'm done.
I thought I had a hormone imbalance and so went to a holistic internist who's an MD and he ran a blood, urine and fecal panel to see what is going on and found my testosterone levels were normal but that my thyroid and Vit. D levels were low, another reason why I've added Vit. D to diet.
I hope these few insights are helpful. Please do share with me if you do find something that works for the long haul... this condition takes a lot of discipline to clear up :(.