Use PDFScissors to crop the page numbers and headings, and convert the cropped PDF.
http://www.pdfscissors.com/
The other way is under the search and replace menu of the Calibre convert page. You can use the wizard (wizard staff icon) to search for page numbering with a Regex expression and replace with nothing.
The easiest way is that you search for a page numbering, select everything from the last <br> before the page numbering till the next normal line, and copy it to the Regex input field.
Example:
ször nem lehetett öt yardnál tovább látni előre, de Jessie nem törődött vele.<br>
- 25 -<br>
<hr>
<A name=26></a>Félrerántotta a kormányt, hogy kikerüljön egy rókát, azután gázt adott. Tekintete végig a bal <br>
You have selected:
- 25 -<br>
<hr>
<A name=26></a>
Now replace the numbers with \d+. The A name= too. \d means number in the regexp.
The regexp expression will be:
- \d+ -<br>
<hr>
<A name=\d+></a>
click on the Test button and it will highlight the result of the Regexp.
Left blank the Replacement Text field and try to convert.