The limiting factor appears to be in your .htaccess file:
php_value post_max_size 1M
The post_max_size needs to be at least equal to the upload_max_filesize, so increase that to 100M. The settings in .htaccess should override the settings in php.ini.
Edit:
If that doesn’t work, and since you have full root privileges, you can modify the main php.ini file. To find where php.ini is located, create a temporary PHP file in your website (i.e. temp.php) containing this:
<?php phpinfo(); ?>
Load the page in a web browser, and look for “Loaded Configuration File” near the top, with a value like /etc/php5/apache2/php.ini (be sure to delete the temp.php file after you view it). Edit the upload_max_filesize, post_max_size, etc, and save the file. Then reload or restart Apache (or whatever web server you run) for the changes to take effect. On an Ubuntu server running Apache, I would use: sudo service apache2 reload
For those who don’t have root access, as typical in a shared hosting environment, you may need to contact your host to find out if (and how) you can make changes to PHP settings. For instance, some hosts allow you to create a php.ini or php5.ini to add settings, which is what a plugin like Upload Max File Size might assume.