I have been using Org for writing research papers for a while, gradually improving my set up to be able to exactly produce the output I want. In this process, I have benefited greatly not only from the resources available on the Org-mode website but also from various people who generously provided solutions to my numerous queries on this mailing list. I felt that it may be of some use if I put together all the pieces and document what I was doing.
I have put the draft for comments at: https://github.com/vikasrawal/orgpaper/blob/master/orgpapers.org It has been written keeping in mind my graduate students as examples of potential beneficiaries of the documentation. Which means that I had somewhat specific requirements in mind. Also, I have tried to write it for somebody who is not familiar with emacs/org-mode and would like to start using the system before investing time in learning the nitty-gritties. That is how I have always managed to entice my students to using free software. I give them a working setup that they can use, and slowly help them learn the insides of it. So the focus is not to provide all the possible options and different ways of customising the output but to provide a specific usable solution. For whatever it is worth, here it is. Pointers to any errors as well as comments for improving it would be greatly appreciated. Also, I would be happy to contribute it to Worg, if people consider it useful. With thanks to the Org community, Vikas