I wrote a Perl script some weeks ago that works on Unix systems but probably is easy to get to work on a Windows system. The script unpacks the lit file, fix the language tag if neccessary and there is also a variable you can set to fix totally broken HTML and incorrectly coded characters (something I had in one book). It also calls mobigen.
It is available here:
http://www.ida.liu.se/~tompe/old-lit2mobi