All your data can be easily transferred between Linux and Windows, see
http://wiki.splitbrain.org/wiki:faq:servermove. Using the DokuWiki on a Stick distribution is probably the simplest way to get DokuWiki running in your Windows network. Just copy it to the hard drive of your Windows server, and add the mapache to your autostart folder. You might want to change the port from 8800 to the more common port 80 in the httpd.conf file.