Siginificant Speed Increase (Upgrade PHP, Disable FastCGI)
So, I re-wrote some code, removed some blocks, changed a lot of things to speed my site up a little bit but was still not satisfied. So, I decided to look at the server configuration itself. In going through my PHP configuration, I noticed that I was still running PHP v5.2 and was in FastCGI mode. I decided to upgrade the PHP version and also disable FastCGI.
With version 5.3 I noticed right away a huge speed increase but decided to upgrade even further and changed it to version 5.4, no FastCGI, Single file. This was significant...the site now runs at least 100% faster if not more. So, if you are experiencing a huge speed decrease in your build, perhaps take a look at your PHP version, and try disabling FastCGI (Don't forget to make any changes that you may have made in previous versions like upload_max_filesize etc.), you might be pleasantly surprised with the results! Like I said previously, not sure what the reason for this increase is as I haven't gone through everything, but it sure seems to work for me.
For now I am sticking with v5.4 even though it doesn't seem to support zend etc and so far there seems to be no issues whatsoever...will update if I run into any errors.
I run PHP in fcgi mode because I need suPHP and multiple versions of PHP enabled. I configured my own server (PS: don't do this if you don't have experience with it).
My websites are usually blazing fast. In your case, I'm guessing it's been a configuration issue which has been eliminated during the switch from fcgi to mod_apache because this means using a different php.ini config file.
For an ultimate speed increase, I'd use nginx as a reverse proxy, and apache to handle the back-end stuff.