#1) print the pdf's to pngs as they are seen with alpha, layers, transparency etc, this cannot be done by ImageMacick convert or pdftoimages
Pdftk combined_to_do.pdf burst output pg_%04d.pdf ImageMacick convert, gs, or pdftoimages don't work as good as inkscape they either don't export the layers or export but with bad quality : #!/bin/bash
Inkscape is the best solution, I quickly made this rather unoptimized batch file that does exactly that and you can play with it and change options.