If the included PDF files( the second problem in the article above) are generated under windows, they can be re-generated to embed all the fonts needed. An alternative way is that convert them into ps files, and then use acrobat distiller to convert the ps files back into PDF files. Acrobat distiller should be configed to embed the required fonts.
In linux, you may also try to convert the pdf file back to ps file using pdftops, and then convert it back to pdf file using ps2pdf14.
Use "convert" to chanage/rotate ps/eps files if necessory. convert -size WidthxHeight -rotate Degrees foo.ps -resize NewWidthxNewHeight foo.(other format)Related links: