> issue 5, is partially asking about issues i had come up when install a few hundred third party plugins.
Installing hundreds of different plugins is likely to cause problems with any system - Moodle, Wordpress, Joomla - any system. Remember the one and only way to be sure that a module doesn't cause a security problem or some other major issue is by not installing it. You might consider installing only the plugins you have an actual use for. Any module you install costs you - it costs you performance, it costs you reliability, and it costs you security risks. So for each, ask yourself "is the benefit I get from having this module greater than the costs?" There are always costs.