Calibre and most other PDF -> non-PDF converters mangle formulas and line graphics. That is inherent to the design of the PDF format.
Your best bet is probably
soPDF, a PDF -> PDF converter that can split pages.
Or you can convert the PDF to a sequence of pictures (for example with
Bullzip PDF printer), refine the images in a graphics program, combine them into a comic file (
cbz) and put this through Calibre.