Haven't gotten to the upgrade yet, still working on merging the 2 branches...

Anyways, I did notice the App_Browser folder did not get renamed to App_Browsers

I'm using the Source zip... Haven't bothered to check the others yet...

As for the other issue with the System.Web.Extensions... 

I haven't verified this in anyway, but I believe the problem has to do with a bug that was in the "Upgrade Framework" web.config merge.

Can you check your web.config before you delete that dll?

The bold bits needs to get deleted, that should get your site going again. I think...

      <dependentAssembly xmlns="">
        <assemblyIdentity name="System.Web.Extensions" publicKeyToken="31bf3856ad364e35" />
        <bindingRedirect oldVersion="1.0.0.0-1.1.0.0" newVersion="3.5.0.0" />
      </dependentAssembly>
      <dependentAssembly xmlns="">
        <assemblyIdentity name="System.Web.Extensions.Design" publicKeyToken="31bf3856ad364e35" />
        <bindingRedirect oldVersion="1.0.0.0-1.1.0.0" newVersion="3.5.0.0" />
      </dependentAssembly>

Also, making sure the xmlns="" bits are removed will allow your portal to run modules compiled for both asp.net 2.x and 3.5 without erroring out due to the version mismatch on the system.web.extensions dll

Ok, I have verified this now, and the web.config is the root cause.

If you clicked the "Upgrade to Current Framework" button in Host Settings on DNN 5.0.0 (or any of the previous RC's), then you probably have bug...

You need to manually edit your web.config, it should be around line number 243ish. I was slightly wrong above (although it will still work), the DNN 5.0.1 method is to add the "urn:schemas-microsoft-com:asm.v1" into the empty xmlns=""

Below you'll find a fully working section.

 <runtime>
    <assemblyBinding xmlns="urn:schemas-microsoft-com:asm.v1">
      <probing privatePath="bin;bin\HttpModules;bin\Providers;bin\Modules;bin\Support;" />
      <dependentAssembly xmlns="urn:schemas-microsoft-com:asm.v1">
        <assemblyIdentity name="System.Web.Extensions" publicKeyToken="31bf3856ad364e35" />
        <bindingRedirect oldVersion="1.0.0.0-1.1.0.0" newVersion="3.5.0.0" />
      </dependentAssembly>
      <dependentAssembly xmlns="urn:schemas-microsoft-com:asm.v1">
        <assemblyIdentity name="System.Web.Extensions.Design" publicKeyToken="31bf3856ad364e35" />
        <bindingRedirect oldVersion="1.0.0.0-1.1.0.0" newVersion="3.5.0.0" />
      </dependentAssembly>
    </assemblyBinding>
  </runtime>