OSX Server Can I delete existing setup & start from scratch

[evan-e-cent]

Using OS X Server 10.5.6 Leopard with multiple virtual domain web sites. Having problems with permissions and keep getting a system error. How can I delete the existing server setup and start again from scratch without reinstalling OS X. Otherwise reset all permissions. Last time I tried it locked me out and I had to reinstall OSX. The server computer is a Mac mini located 3 hours drive from here. Several features including remote start are not available on the Mini. Thanks.