I'm sorry, I made a mistake, the file should be installed by SmithCart, but depending on your hosting environment and Ajax configuration, web.config may require manual modifications to make it work properly. Different Ajax versions have always been a problem for ASP.NET. If SmithCart forced its version it could break other modules. On the other hand if another module forced its version, it could break other modules including SmithCart.
The clue here is "manifest definition does not match the assembly reference". This means your web.config is configured with a specific version that is different than the file.
You will probably need to add this to the assemblyBinding section in web.config
<dependentAssembly>
<assemblyIdentity name="AjaxControlToolkit" publicKeyToken="28f01b0e84b6d53e" />
<bindingRedirect oldVersion="1.0.20229.20821" newVersion="3.0.30930.28736" />
</dependentAssembly>
I hope this is of some help to you.