I dropped the patched file into /usr/local/texlive/2014basic/texmf-dist/tex/latex/tools and /usr/local/texlive/2014/texmf-dist/tex/latex/tools/, renaming the original, as I was not sure which one was the right one. I'm getting much closer! So far, all of the graphs are OK except for one xyplot() that for whatever reason starts about 2 inches above the bottom of the page and paints under the page number while running off the screen. This page also has a ggplot graphic as well as a pander table, while simultaneously dropping about 50 words of text. 

Was there an issue with the patched template when you have stuff before and after the pandoc table?