Changing OS from Windows to Ubuntu without breaking everything

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http://serverfault.com – I purchased a dedicated server a few months ago, and based off the advice of the only person I knew with any knowledge of servers, chose a windows based server. We came to this conclusion as we have both done a couple of Windows Server qualifications, unfortunately I can't really remember any of it. Unfortunately, neither of us have much experience of windows as a webhost, so it's been giving us a lot of grief with permissions and poor rewrite rules and generally sucking just as much as windows always does. Through my web hosting companies control panel, I can change the operating system. (HowTos)