Have you checked out
k2pdfopt that converts complex pdf:s to a pdf suitable for Kindle. Works very well and I recommend it strongly!
No installation needed. Just drag the pdf file(s) that should be converted to the k2pdfopt.exe. The converted files comes in the same directory as original files but with _k2opt added to the filename. There are many options in the software but the default options work most often good enough for the 6-inch Kindle.