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Not something you can really do within Calibre, but here are two options:
1. Do the conversion from PDF to EPUB again, but this time specify a debug folder in the conversion options. After the conversion you'll find intermediate HTML files from the PDF conversion. You can then take the HTML file and split appropriately in your favorite text editor, load the split HTML files into Calibre as the individual books, and convert those to EPUB. Requires knowledge of HTML, because you can't just cut it in the middle.
2. Try an epub editing tool like Sigil. I don't think it has direct functionality for splitting an epub into multiples, but you can manually go through and change metadata, delete files you don't need from other parts of the books, and then "Save As" your new epub. Do this for each book in the larger whole. Tedious, and you have to be careful not to accidentally save over the original EPUB, but it should be possible to do.
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