AH00082: an unknown filter was not added: PHP

Должно быть так

/etc/apache2/apache2.conf

AddType application/x-httpd-php .php
AddType application/x-httpd-php-source .phps

А не так

/etc/apache2/mod-available/php5filter.conf
<Files *.php>
       SetOutputFilter PHP
       SetInputFilter PHP
</Files>

Делаем так

#<Files *.php>
#      SetOutputFilter PHP
#       SetInputFilter PHP
#</Files>

php configure 5.3

./configure --with-apxs2=/usr/bin/apxs --enable-mbstring --with-mysql=/usr/bin/mysql_config  --with-mysqli=mysqlnd --with-pdo-mysql=mysqlnd --with-config-file-path=/etc/php/