Seems to me you have bought a Volvo and are trying to modify it into a Mercedes. Both are good, both do the same job very well - but they are different.
If you have very specific requirements as you have outlined, there are many distros that have "servers" that you can manage yourself - especially with Webmin, VNC and/or SSH.
SME provides a very stable (Stable is IMPORTANT) environment which is managed through the server-manager interface. If you make changes some other way, next time there is an update, your changes are probably going to be lost. (There are ways of making them permanent by modifying the templates, but you have to know what you are doing and be prepared for less support in the forums as you drift away from the standard.)
Remember, if you want to live on the bleeding edge of software, with the latest versions, then you are opting for an exciting life! If you want a rock-solid system, with no-fuss management, stick with the stable versions. That is what SME/CentOS 4 is about.
Good luck - hope you have success with what you are trying - If nothing else, you are learning lots (which we all need to do).