Hi all, 
Thanks for the replies - we ended up with a similar solution to FroggEye.. though did all the work in the new app's web.config. Used Removes and Clears .. for example (note, these are incomplete snippets):
      <assemblies>
        <remove assembly="System.Web.Mvc, Version=3.0.0.0, Culture=neutral, PublicKeyToken=31BF3856AD364E35" />
    <pages controlRenderingCompatibilityVersion="3.5" clientIDMode="AutoID">
      <namespaces>
        <clear/>
      </namespaces>
    </pages>
    <httpModules>
      <clear/>
    </httpModules>
    <httpHandlers>
      <clear/>
    </httpHandlers>
  <system.webServer>
    <modules runAllManagedModulesForAllRequests="true">
      <remove name="RoleManager" />
      <remove name="XHtmlModule" />
      <remove name="CMSApplicationModule" />
      <remove name="UrlRoutingModule" />
      <remove name="Detector" />
      <remove name="ErrorHandlerModule" />
    </modules>
    <handlers>
      <remove name="MetaWeblogAPI" />
      <remove name="ChartImageHandler" />
      <remove name="UrlRoutingHandler" />
    </handlers>
Everything is working nicely now.