Yeah my snake always gets blue eyes a few days after turning pink. So I don't think there's any worry there. Mine has never been aggressive while shedding but any snake can act differently. I've seen some snakes that were pretty grumpy cause of shedding. I agree with Running Elk though, I wouldn't handle her for a little while. As for the brownish spots, I'd wait and see if they go away when she's done with shedding. Sometimes I've seen early stages of scale rot that look kind of similar, but I don't think that's what it is. It sounds like you're taking good care of her. I think it will be fine when she sheds. And there is also the option of feeding her another rat too. Hope that everything gets better!