There is no good way to convert a math text to any reflowable format. With MOBI, in particular, the equations have to be replaced by images. This is hard to do for the author of the ebook, and impossible for an automatic PDF converter.
Your best bet is to improve the PDFs to make them easier to read on the Kindle as PDFs. If they are double column they can be split into one column, and the margins can always be stripped. Two possible tools are
soPDF and
BRISS. These are PDF to PDF converters. There are also PDF to image (in MOBI or in PDF) converters, one of the most popular is
PDFRead.
A 6" screen isn't good for PDFs, so in the end all of these approaches could fail to produce acceptable results. A Kindle DX would handle PDFs better, even though the K3's PDF capabilities are improved somewhat over the KDX.