Going from an installation profile to vanilla Drupal I currently am using the Acquia Drupal installation profile on a site, and I want to convert it to a vanilla Drupal install.  Other than cross referencing the modules that come with the profile, and making sure you download those from drupal.org and putting them into sites/all/modules, are there anymore steps that would need to be taken besides your regular update instructions?
Once a Drupal site is installed, it doesn't really matter which installation profile you used. The only difference is that it's possible to use modules and themes that are located in the profiles folder. So in that sense you are running vanilla Drupal.

If you want to disable the possibility to use the modules from the profile you need to, once you have added the modules to sites/all, set the installation profile to "standard". The easiest way to that is to use drush:

$ drush vset install_profile standard