find . -name "*.pdf" -exec pdftops -eps {} \;
The other difficulty was related doflattening the tex files and including the bibliography rather than the bib file. So I would not have to deal with this nonsense again, I wrote a short script to do this for me. I hope to expand this in the future to also handle the renaming of the figures in order of appearance; but for now that remains a manual step. The scrip is attached to the end this post