Apache PHP module vs. Apache with PHP?

I'm on a VPS and am pretty happy, but sometimes the site gives a Network Timeout:
The server at XXX.com is taking too long to respond.

I'm using a standard cpanel setup because I'm comfortable with adding domains/emails that way - actually have scripts programmed to do tasks automatically using cpanel.

I was thinking about:

  • Having Apache complied with the PHP module. (Apache would have PHP built in, instead of calling PHP-CGI - PHP as a separate program).
  • Trying GCID (found out about it here but it's from 2005.)
  • Stripping out other services (not sure what?)
  • Trying out Ngenix (but would need to be able to test in parallel with Apache.

My biggest concern is that PHP complied into Apache is supposed to have tight security and affect if/how files can be saved to the server.

Anyone want to share their experience/suggestions?