Many of the steps where taken from the Microsoft knowledgebase article 828810 - "How to enable an ASP.Net application to run on a SharePoint virtual server" http://support.microsoft.com/?id=828810

• Follow the regular installation instructions for FlexWiki - InstallingFlexWiki or DeveloperSetup
• Configure SharePoint:
• Click Start, click Administrative Tools, and then click SharePoint Central Administration.
• In the Virtual Server Configuration area, click Configure virtual server settings.
• On the Virtual Server List tab, click the virtual server that you have to add the excluded paths to.
• Under Virtual Server Management, click Define Managed Paths.
• In the Add a New Path section, type the path that you want to exclude in the Path box - i.e. /flexwiki
• Click Excluded Path, and then click OK.
• Close the SharePoint Central Administration web page.
• Explore to the root folder of the default web site - usually c:\inetpub\wwwroot
• In order to allow FlexWiki to run with debugging and user session state, we have to configure IIS to allow the flexwiki virtual directory to ovveride the permissions, etc. that the SharePoint web.config file applies. To do this, edit the end of the web.config file (with notepad, etc.) so it looks like:

              ...
            </system.web>
          <location path="flexwiki" allowOverride="true"/>
        </configuration>

• Save and close web.config
• Configure FlexWiki web.config:
• Explore to the root directory of the flexwiki virtual directory - i.e. C:\prj\FlexWikiCore\FlexWiki.Web (this was the location of my dev install, however I tested these instructions on the binary install as well)
• Open the web.config file and edit the end of the web.config file (with notepad, etc.) so it looks like:

        <!-- Setup the PageHandlerFactory to process all requests. This will override the SharePoint HTTPHandler. -->
        <httpHandlers>
           <add verb="*" path="*.aspx" type="System.Web.UI.PageHandlerFactory, 
                System.Web, Version=1.0.5000.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a" />
           </httpHandlers>
           <!-- Set the trust back to Full. WSS configures a very restrictive trust policy that 
                does not allow most applications to run correctly. -->
           <trust level="Full" originUrl="" />
           <!--
           Enable the modules that you must have for your program to run.
           If you receive the following message:
           Parser Error Message: The module '<moduleName>' is already in the program and cannot be added again
           You can remove the modules that are mentioned in the error message. The SharePoint web.config already 
           includes the module for OutputCache and WindowsAuthentication so you do not have to add them here.
           -->
            <httpModules>
              <add name="Session" type="System.Web.SessionState.SessionStateModule"/>
              <add name="FormsAuthentication" type="System.Web.Security.FormsAuthenticationModule"/>
              <add name="PassportAuthentication" type="System.Web.Security.PassportAuthenticationModule"/>
              <add name="UrlAuthorization" type="System.Web.Security.UrlAuthorizationModule"/>
              <add name="FileAuthorization" type="System.Web.Security.FileAuthorizationModule"/>
            </httpModules>
          </system.web>
        </configuration>

• Save the web.config
• FlexWiki should now run.