Double-dipping to add: Calibre recommends not using PDFs as your source format if at all avoidable.
I feel like I should emphasize that it's not just that the format is ill-suited to conversion, but that Calibre's conversion routine for it is particularly poor; I quit using it when I noticed that the output was frequently truncated early.
Better conversion options:
All of those could potentially mess up equations and the like, though; so you might just have to deal with it or get a bigger device.
If it's worth saying, but not worth its own post (even in Discussion), then it goes here.