1. You will get a word count of zero for PDFs that contain image pages (that haven't been OCR'd).
2. With the change I have mentioned in post right before yours the next release of the plugin will treat a zero word count as an "error" situation in that it will just write a message to the log and not write zero into the custom column.
3. Any issues to do with PDF conversions are *nothing* to do with this plugin. They are calibre/PDF library issues. If you have a specific pdf that causes a fault with this plugin, you will almost certainly get the same fault when you use calibre to do a PDF-> EPUB conversion. As such follow the official calibre support routes - you can raise a ticket, attach the PDF in question and it is possible someone will take a look at it. If calibre can convert the PDF without crashing, so should this plugin.
4. Keeping the temporary PDF to count pages is not going to happen. If you want an EPUB version, convert before you count pages, and this plugin will then work with that EPUB. As has been well documented PDF-> EPUB versions generally suck and require much editing and tuning to look anything like the original - what this plugin produces is designed only for the purposes of estimating a word count, not human readability.
5. As per my answers in 3, I'm afraid the log isn't something I can do anything about.