Papers2, Word, and footnotes

Hi, so I’m working on a longer term paper and I’m having trouble exporting from Scrivener to Word for final formatting. My workflow is as follows:

  1. Draft to near-final form in Scrivener, which includes font changes and footnotes. Insert in-text citations and bibliography via Papers2 (magic manuscripts).
  2. Export via RTF to Microsoft Word 2011. Make any final necessary changes.
  3. Invoke Papers2 MM (in Word 11) to format citations and bibliography.

At this point I should have a final document in whatever draft form I need, but this isn’t the case. First, my fonts seem to change back to a default Times New Roman. But most troubling is that my footnotes suddenly disappear. Am I doing something wrong? Does anyone use this workflow? Any tips would help greatly. Thanks!