Gracie and
Libby are darling names together. Like you, I prefer them as nns.
I like
Libby from either
Elizabeth or
Liberty. I don't think
Grace and
Liberty are too themey together because (1) two names do not a theme make, more of a coincidence; and (2) using nns on a daily basis keeps any supposed theme from being obvious.
That said, I'd prefer
Elizabeth, nn
Libby. But
Liberty, nn
Libby would be nice as well. Have you considered
Graciela, nn
Gracie? Just a thought.