The thing with the eyeballs being black may have to do with a bit of geometry over the eyes to help simulate specularity. On M2 I believe it's called "Eyeball" and on the Millenium figures
I think it's LeftCornea and RightCornea. Set the Alpha on both of those to transparent and it should go away.

I've had a similar problem with those blasted UpperEyebrows that you're having. They even appear in ToonPro. One solution might be to import the figure using Native Import so you have better control in overriding the default settings for Non-Photo rendering. Override the defaults and then set them to full transparency and it ought to work. In theory.

I hope that helps! Good luck!