In terms of physical files (WordPress core or plugins), the core setup of a WordPress project is straightforward:

- The project root contains wp-admin, wp-includes, wp-content, and the main core files.
- wp-content/ contains your custom code - themes, plugins, uploads, backups, whatever be it.
- uploads/ are grouped by years and months (for better accessibility).

If you're struggling with the search itself, make sure you're not overcomplicating your product with dozens of random plugins that you don't need. Keep it simple. Each plugin has its own purpose, which makes it easier to find the right function or class.

Using a professional IDE like PhpStorm, Eclipse, Netbeans will help you search thoroughly. On Mac/Linux, you can study grep or ack and craft complex search queries for whatever you need (including pipelines of stacked commands).

In terms of your media uploads, there are plugins that let you organize the media in a sensible manner. If you've integrated with AWS S3, creating buckets for certain files may be a better approach, too.