As said, you will be able to get new diplomas (probably, check with the universities), but not the past publications. They're said and done, and you will have to refer to them as your old self if you want to use them. The key is getting the PhD, which is cool, done after your name change. That's what people will use as a professional reference. And all future publications will be under your new name.
As for your CV, you can list them and let people ask you about it, which you can say it was your old life. I wouldn't put the change on the CV except as a label "previous publications" and no mention of name or gender change. Let folks ask or connect the dots.
Good luck with the PhD. I stopped at the MS degree, the need for life and work got in the way. And just curious, what's the (general as not to give away too much) subject of it?