You need to shim the factory for every type parameter. Assume you have the three Service contracts 'IService0' 'IService1' and 'IService2'.
Then you need to setup the shims like this:
ShimChannelFactory<IService0>.AllInstances.CreateChannel = (_) => { return new Service0Mock(); }
ShimChannelFactory<IService1>.AllInstances.CreateChannel = (_) => { return new Service1Mock(); }
ShimChannelFactory<IService2>.AllInstances.CreateChannel = (_) => { return new Service2Mock(); }