Why don't you trust Calibre to convert the PDF file directly?
Also, there's an ePub editor called "Sigil" that lets you create/edit directly in the ePub format.
If you want to create a mobipocket book WITHOUT using software, try this site:
http://www.beam-ebooks.de/tools/convert/index.php
Copy/paste the text from your HTML file into the textarea and click the
Mobipocket Ebook erstellen button. It'll work for a while, maybe even tell you that the script is slow/dead, but soon you'll get a PRC file which, I believe, can be renamed to MOBI in case that's what the Kobo Reader requires.