When you rev up your metabolism you use more nutrients. You could have some other underlying deficiencies causing your problems. Make sure you're taking all the co-nutrients. Try salt flushes to see if it helps the inflammation/pain.
Also you brought in two factors -- new diet and iodine. I'd blame the diet. Starving fungus can cause them to grow deeper roots into your flesh to get at nutrients (you ALWAYS have blood sugar)-- try Borax therapy as discussed here instead.
Lastly -- practical help for your stomach -
1. Try drinking less/no water/liquids near meals.
2. Try using ACV supplementation.