Yeah, I got it working, but it's a very manual process. There's no nice neat solution.
As for figuring out the CSS files, read up on custom skinning, and jsut include the necessary CSS files. http://www.telerik.com/help/aspnet-ajax/introduction-how-skins-work.html
All files you include this way will need to be listed in your AppCache manifest.
Also, for even if you go through disabling JQuery, there will still be a couple references to WebResources.axd. I haven't been abel to figure out how to get rid of this properly. The best way I found to ID these is with Chrome's Developer Tools. Follow these steps:
Load the page online with the AppCache Manifest so everything gets cached.
Open Developer Tools and go to the "Network" tab.
Anything that shows up in RED text is a file that couldn't be loaded, and thus missing from AppCache manifest.
There might be a few that are still WebResource.axd references. You'll find these links stay pretty much static. The only time I've found it changes is when you update/move the Telerik dlls. Still if you muck about with the DLLs that they reference, (in my case AjaxControlToolkit, and System.Web.Extensions) the links will changed, and updating Telerik might also change them.
Jsut add them to your Manifest and be aware they can change, but it probably won't happen on production unless someone updates a referenced DLL