How can I prevent users from downloading my course files such as pdf or word-processed documents?
You can’t. There are various ways to make it more difficult for them, and you can make them sign a declaration not to download them, but determined users can always find ways to save or download your course materials. If all else fails they can make a screencast or screenshot. If it is essential for you that users do not download your course materials then do not offer the materials in your course.
How can I stop uploaded files from being cached when I update them?
By default, LMS adds a “cache-control” header to all files that are sent. The default period is 24 hours. You can reduce this or eliminate it entirely (set to zero) by adding the following line to your config.php (default value is shown).
$CFG->filelifetime = 86400;