Elisabeth and Amelia are both lovely! While I'm crushing more on Amelia lately, I know Elisabeth is my true love, so I'll go with that. I think Elisabeth Amelia would be nice, or Elisabeth Harper? I also really love the idea of Elisabeth Noelle, Elisabeth Sophie, or Elisabeth Violet. I really, really love Amelia June of your options, though--I think that's so pretty! I think Molly and Amelia is darling, but still, Elisabeth is my favorite. :)
I like Amelia, but don't think you can use it with Molly. They'll get too tangled in everyday speech. Elizabeth is great, of course. Libby and Molly.
And while Paige isn't one of my favorites, I like the way it balances out the sometimes too-traditional Elizabeth. Elizabeth Paige has a nice ring. And Paige is similar to Blythe.