So, want to convert a pdf for kindle reading with formatting? I certainly did, and this post
https://www.mobileread.com/forums/showthread.php?t=16636 on these fine forums gave me the way. So all that needs to happen to get it done is make the pdf image based rather than text based. This does have a cost, the output is not searchable, and there are no links for a table of contents, but for scientific papers and other highly complex formatting situations, I think it's worth it until they get us something better.
Now, unfortunately most PDF tools don't support making non-searchable PDFs because it's the reverse of what one normally wants PDF for. Luckily there are tools meant for other things

.
Imagemagick can convert from pdf to just about anything, and from just about anything to pdf, but because its internals use rasterized images... you got it, every pdf that comes out is image based! So
Code:
convert -density 120x120 <source>.pdf <output>.pdf
generates a nice image based pdf file in a few seconds. Send that through the conversion email address for your kindle and even the most complex (correct) pdf will look just right on your kindle.
Now, the qualification in the previous sentence is because imagemagick has a bug related to certain unsupported forms of compression, so every once in a blue moon this can fail, but for the most part it produces a beautiful (though unfortunately large) output.
Also, if you find that the text is a little faint or blurry after the conversions, try upping the density, it will go as high as you want, but increasing it will also make the file larger, so keep that in mind. (1200x1200 took 4GB of ram before the conversion crashed...

so really, be careful)