conversion always fails (site.py)

I run portable calibre on Windows. The database holds about 400 book records. Calibre conversion from any format to mobi (and to other formats) always fails with this kind of log:
full log
This portable calibre, let's call it calibre1, has a few extra plugins installed, and a custom column (of type 'date').

I downloaded and expanded another portable calibre, let's call it calibre2, added the same pdf file to the database, and successfully converted that pdf file to mobi.

At this point I pointed calibre2 to use calibre1's database and attempted to convert another pdf file. This time also calibre2 failed converting the file and output exactly the same error log.

So I'm thinking that calibre1's database is somehow corrupted to the point that no file can be converted to another format.

Questions/Help Req:
1) How can I fix calibre1 so that I can successfully convert ebooks?
2) If fixing calibre1 entails rebuilding the whole ebook database, what's the best/quickest way to do it? Will I lose any metadata in doing so? Will the library folder structure change?
3) Where does calibre keep all those .py files that are referenced in the error log, like site.py, etc. I searched through calibre1's folder but couldn''t find any of them.

Thanks in advance