The hot flushes could be due to low progesterone or high estrogen, or even a histamine reaction. And honestly, with diet, you just need to keep track of what you eat every day (like a food journal) and possible allergic reactions to environmental things or even body lotions (to see if that helps with itching) for at least 1-2 months. Some pimples can take up to 2 weeks to come to the surface, so it's hard to know what caused them in the first place especially if it's food related. I had a pretty clean diet with lots of fruits and vegetables, then I realized I needed to cut down on the fruits and even veggies/fruits I used to eat every day thinking they were good for me (like tomatoes). I discovered I was getting a histamine reaction whenever I consumed/ was exposed to many histamine triggers like humidity, body lotions, tomatoes, cider, but it took a while to make this connection and then it took some blood work to confirm it. So you just have to give it time and find a diet that works for you, there is no quick fix for putting your body through stress and poor diet. I'm not being judgmental, trust me I have been there and abused my body to no end and now I'm paying for it! Just try not to go crazy with elimination diets, go slow and be patient. Check out my log for my trial and error to discover my sensitivities - I posted a scary before pic today.
As for soy milk, it depends on your body....personally, I have never broken out from organic unsweetened soy milk and in fact I think it helps my skin in small quantities. It's supposed to be estrogenic, so I try to balance it with magnesium to help raise my progesterone.