Until its changed in your php settings, then nothing you do in Moodle can override those. They are the core settings for how your webserver works and Moodle is restricted to those settings BEFORE it can apply any of its own. Those php settings should not be the 5th place to check and to adjust, they need to be the 1st. As for your .htaccess working/not working or a custom php.ini in your public_html folder, again those are webserver issues to take up with your hosting provider.
They don't need to know Moodle (although it obviously helps) as, in the first instance, these are webserver php settings that are necessary before Moodle does anything, and Moodle can then only work within the webserver settings and does not (cannot) override those php.ini settings itself.
Get those core webserver settings sorted and THEN look at the settings within Moodle - site policies, course and assignment as required.
Unless changes were made to your webserver configuration at the same time as you upgraded Moodle, then your upgrade should not have had any impact on those php.ini values or your .htaccess file.