Yes, I pretty much did what was recommended. But the problem persists. I had found some crashed tables in some databases and thought fixing them would do it but no. I backed up the server and installed the latest mysql and couldn't get anything to connect to it. So I restored. So just rebooting the server fixes everything for a while as a temporary fix.
So I'm sure it's a mysql fail because I have the following errors:
bash-3.2# sudo /usr/local/mysql/support-files/mysql.server restart
ERROR! MySQL server PID file could not be found!
Starting MySQL
ERROR! The server quit without updating PID file (/usr/local/mysql/data/example.com.pid).
2016-02-20 18:26:59 18279 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2016-02-20 18:26:59 18279 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
160127 06:52:32 mysqld_safe A mysqld process already exists
160127 06:52:42 mysqld_safe A mysqld process already exists
And in activity monitor there is only one such process.
In your mention of "MySQL included samples" do you mean the things inside mycnf that are commented out?
Also some strange Apache items:
Ive had this error about half dozen times over the last four weeks and the server sites slow to a crawl:
[Tue Feb 23 19:51:19.224849 2016] [mpm_prefork:error] [pid 528] AH00161: server reached MaxRequestWorkers setting, consider raising the MaxRequestWorkers setting
And I found that setting to be 256, but wasn't sure what to increase it to.
The other thing is that the log files in apache2 keeps changing permissions by themselves so that clicking on them in console says "you don't have permission to view". So I select the logs/apache2 directory and hit "apply to enclosed items". But then I have to do this again after couple days.
I'm thinking of just exporting all users, email, websites and reset the server to it's freshly installed state. If I do that, think it would be better to go to El capitan?
As always, any light anyone can shed in these is appreciated. Thanks!