I'm getting wait times between 1.4 seconds to 2.9 seconds.
I should only be waiting for the RTT + 160 ms, which for me is around 350ms for a server response.
I've done a little profiling with the tools I know, but I can tell that Apache is not at fault here.
The causes would therefore be somewhere like in too much execution, such as something very heavy, (an example I can think of is ZenCart with PHP), or there's a problem with the MySQL server, or socket between PHP and the MySQL server.
I would suggest, temporarily using xdebug to grab a callgrind in a controlled environment
So, what I mean is that you have a subdomain with any random highly unguessable name, which runs a different version of php.ini
So, add something like ilikewafflesandbaconwbbq.1emulation.com as an entry as a virtual host in the apache configuration files, and then make a duplicate of the production php.ini, and make a new directory for debug uses.
Then inside that virtualhost entry.
<virtualhost 188.8.131.52:80=""> [...] PHPINIDir /var/debug/php [...] </virtualhost>where there's a php.ini inside of the /var/debug/php/ folder.
In this php.ini, the entry for xdebug would be enabled.
Make sure to set xdebug.profiler_output_dir to a directory where it can be grabbed via ftp
More information can be found at http://xdebug.org/docs/profiler
I wish you the best in this endeavor, but having a graphics which shows where the most time takes place really can help you find the cause.