Unfortunately you're in uncharted territory with advanced configurations needed for both your CDN (Cloudflare) and your web server (Apache).
UBB.threads is out of the box designed for default web server configurations, and it works for most users; however UBB.threads is a basic web application and we just assume your server is configured to run basic web applications. We cannot provide support for 3rd party services such as CloudFlare, or offer much advice for tuning your Web Server on these user to user forums, and you would likely require hands on toying with configurations for compatibility with such unique requirements such as you're needing for your forum.
Out of curiosity, why do you want users submitting such large files?
