To understand it better, I recommend you just check out the sequence of calls that happen in the Bootstrapper base class Run() method.
But to answer your question, the sure fire way is to override Run in your bootstrapper, call the base.Run() method and then put whatever code you need after that as the stuff that has to happen after the Shell and Modules are initialized. Just realize that does not guarantee they are completely finished loading and being presented on screen. Only way to be sure of that is to handle Loaded events in the Shell itself and in whatever Module screens are loaded by the Initialize methods in the Modules.
But to answer your question, the sure fire way is to override Run in your bootstrapper, call the base.Run() method and then put whatever code you need after that as the stuff that has to happen after the Shell and Modules are initialized. Just realize that does not guarantee they are completely finished loading and being presented on screen. Only way to be sure of that is to handle Loaded events in the Shell itself and in whatever Module screens are loaded by the Initialize methods in the Modules.