Have you tried assembly redirection in your .config file for those references?
<runtime>
<assemblyBinding appliesTo="v2.0.50727" xmlns="urn:schemas-microsoft-com:asm.v1">
<dependentAssembly>
<assemblyIdentity name="System.Web.Extensions" publicKeyToken="31bf3856ad364e35"/>
<bindingRedirect oldVersion="1.0.0.0-1.1.0.0" newVersion="3.5.0.0"/>
</dependentAssembly>
<dependentAssembly>
<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>