One other thing, make sure you build everything from the source.I was right there with you until this bit of crazy.
Do not build everything from source. You're just asking for trouble when you do. You lose so many really important features of modern Linux distros when you do this, that I can't believe people are still suggesting it as a sane practice for production servers.
If you install from source you won't be able to update quickly and easily via apt-get or yum when a security update comes out...you'll have to rebuild. But, you probably won't even know a security update exists until it's too late. If you don't keep copious and specific notes about what your custom build does, and why you did it that way, you will forget a flag or overwrite or lose a config file, and it will break something next time you roll out a new version.
The performance benefits are probably negligible, and in my many years experience cleaning up amateur maintained systems, it is just as likely to be negative as it is positive. You probably know dramatically less about the package you're building than the maintainer of the OS package, and you're more likely to make mistakes than they are. Those mistakes could have security implications, performance implications, or stability implications.
Certainly, if you are the maintainer of some piece of software, you might want to replace it. I've never run a system without at least a few custom builds...but the custom pieces are usually software that I am one of the core maintainers of, and I know it better than just about anybody. And, when I do run custom software, I tend to build an RPM or deb of it, and setup a local yum or apt-get repo, so that when I need to replicate my production machine, I can do it quickly and consistently.