As a retired surface Nuke, I can't answer most of the questions about the boat. However, as far as what he will do as an ELT, there is almost no difference.
Shutdown or critical, he will be doing samples, both primary (up to a certain point) and secondary, as well as Radcon (Radiological Controls) surveys.
Quals in the yards, at least on surface ships, were handled with simulations, walk throughs, discussions and even underway periods on other carriers. I imagine the process would not be much different for our submariner brothers.
Congrats to him and thanks to him for volunteering to serve his country!