The first question is, why apt-get install worked, if you wand to dou an update, because the command herefore is after and apt-get update
It seems that mod_php is not properly installed andy that's why he's telling
Invalid command 'php_admin_flag', pe
So I would try stop the apache if running, and afterwards take a look with
ps aux | grep apache if processes of apache are still running.
If your config still exists, backup it, then I would reinstall all things you wanted to upgrade regarding apache2 and see if that helps...