Scanner Questions

Can you suggest a list of files and directories to exclude?

This is purely dependent on the individual setup and is usually never the same for all installations.
The best way to determine which files change often as part of normal operations is to do a few manual scans (when you know you haven’t physically changed any files to your system) spaced a few minutes apart.

This should reveal any regularly changing files.

For instance in the W3 Total Cache plugin, you might see the following file which changes often:
cache/config/master.php

Hence you would enter the above dir/file string in the exclusion settings.