As someone has already recommende before ,the best way to address this issue is to install a sample site and then pointing the application folder path to your published site.For manual installation the issues lies in web config.To be presice you have to add in few extra http handler in the web config for IIS 6.Please check sample httpModules and httpHandlers section for IIS 6 web config.
<httpModules>
<add name="InitializationModule"
type="EPiServer.Framework.Initialization.InitializationModule, EPiServer.Framework" />
<add name="FirstBeginRequestModule"
type="EPiServer.Web.InitializationModule, EPiServer" />
<!--<add name="BasicAuthentication" type="EPiServer.Security.BasicAuthentication, EPiServer" />-->
<add name="Initializer"
type="EPiServer.Scheduler.Initializer, EPiServer.Scheduler" />
<add name="WorkflowRuntime"
type="EPiServer.WorkflowFoundation.WorkflowSystem, EPiServer.WorkflowFoundation" />
<add name="UrlRewriteModule"
type="EPiServer.Web.UrlRewriteModule, EPiServer" />
<!--<add name="EventSubscriberHostModule" type="EPiServer.EventSubscriberHostModule, EPiServer" />-->
<!--<add name="IIS5WebServicePostModule" type="EPiServer.Web.IIS5WebServicePostModule, EPiServer" />-->
<add name="ScriptModule"
type="System.Web.Handlers.ScriptModule, System.Web.Extensions, Version=3.5.0.0, Culture=neutral, PublicKeyToken=31BF3856AD364E35" />
<add name="ShellRoutingModule"
type="EPiServer.Shell.Web.Routing.ShellRoutingModule, EPiServer.Shell" />
</httpModules>
<httpHandlers>
<add path="TrackerHandler.ashx"
verb="*"
type="EPiServer.Trace.CMS.Handlers.TrackerHandler" />
<!--Static files served by EPiServer.Web.StaticFileHandler will have cache information added to Response headers
so clients can cache files according to passed header information.-->
<add path="*.png"
verb="GET,HEAD"
type="EPiServer.Web.StaticFileHandler, EPiServer" />
<add path="*.jpg"
verb="GET,HEAD"
type="EPiServer.Web.StaticFileHandler, EPiServer" />
<add path="*.jpeg"
verb="GET,HEAD"
type="EPiServer.Web.StaticFileHandler, EPiServer" />
<add path="*.css"
verb="GET,HEAD"
type="EPiServer.Web.StaticFileHandler, EPiServer" />
<add path="*.js"
verb="GET,HEAD"
type="EPiServer.Web.StaticFileHandler, EPiServer" />
<add path="*.gif"
verb="GET,HEAD"
type="EPiServer.Web.StaticFileHandler, EPiServer" />
<remove verb="*"
path="*.asmx" />
<add verb="*"
path="*.asmx"
validate="false"
type="System.Web.Script.Services.ScriptHandlerFactory, System.Web.Extensions, Version=3.5.0.0, Culture=neutral, PublicKeyToken=31BF3856AD364E35" />
<add verb="*"
path="*_AppService.axd"
validate="false"
type="System.Web.Script.Services.ScriptHandlerFactory, System.Web.Extensions, Version=3.5.0.0, Culture=neutral, PublicKeyToken=31BF3856AD364E35" />
<add verb="GET,HEAD"
path="ScriptResource.axd"
validate="false"
type="System.Web.Handlers.ScriptResourceHandler, System.Web.Extensions, Version=3.5.0.0, Culture=neutral, PublicKeyToken=31BF3856AD364E35" />
<add verb="*"
path="*.mvc"
type="System.Web.Mvc.MvcHttpHandler, System.Web.Mvc, Version=1.0.0.0, Culture=neutral, PublicKeyToken=31BF3856AD364E35" />
<add verb="*"
path="UrlRouting.axd"
type="System.Web.HttpForbiddenHandler, System.Web, Version=2.0.0.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a" />
</httpHandlers>