From a recent post on astrobites, general submission guidelines and checklists for the Astrophysical Journal and arXiv. Most useful was a program linked through the article that takes an input latex file, bib (.bbl) file, and its figures and does the following:
-Removes all commented text
-Places bib items in latex file
-Renames figures sequentially IN latex file and creates new files
-Arranges all material in a tarball