bibliography change output

I have three querstions concerning some options I did not manage to find.

I am working in reference manager 11. I am using the Molecular Microbiology output style for my library and managed to adjust it to my preferences. However, I did not manage to align (justify) my bibliography.(now aligned to the left) How can I change this to align justify.

Secondly, How can I change the sorting order of my library. Now it is set as  last name firts author and last name second author. This should be  last name first author, year of publication.

Thirdly, I want ignore prefixes of last names when sorting the database. For instance, de Vries should be sorted at the V and not at D. 

Please note that I don’t want to change the citation in the text which should be …  de Vries et al., 2009 for instance

Your input and suggestions are highly appreciated…