How to control CSS cascade?
The theme layer loads after your module has, so you won't be able to modify that part yet. I think you can just set the weight on your functions: http://api.drupal.org/api/drupal/includes%21common.inc/function/drupal_add_js/7

Or just rename your ID's and classes to be specific to your module to reduce conflicts. I usually would name my ID's or classes nothing to generic, usually a shorthand for the name of the module then the name of the id or classes i want to reduce conflict.