Honestly, I like them all.
My personal preference, just based on what I personally like (not taking your meanings into account) is Elizabeth Ann followed very closely by Josephine Ann. Eliza isn't my favorite nn for Elizabeth, but that is not a huge deal. I love Josie.
That being said, use the name that you have loved the longest. When I was pregnant with DD I went back and forth with a handful of names but ultimately went with Katherine because it was the name I had loved for the longest. I knew that if Kate was my only daughter that I would regret not using the name for her one day. And 3.5 years later I can say with certainty that I would have regretted using the other names on my list (because, while I liked them at the time my love has faded).
Because it seems that biblical meaning is important, could you do Margaret Elizabeth or Margaret Josephine? You could even do Margaret Ann Elizabeth if you wanted. Call her Mae. hehe.
I do not like Margaret Marian. It just looks too similar and matchy and I don't like the aliteration in this case.