Spent a week in Paris with my 20 year old daughter a few months ago. I booked the Eiffel Tower as you did, booked my time slot at the Louvre and prepaid the audio devise (didn't buy the museum pass until we landed at the airport), booked an Eating Europe tour in advance as specific days sometimes fill, and booked a crepe making class. No need to book the boat trip, we just walked up 20 min before the scheduled departure. We also booked Fat Tires Bike Tour of Versailles in advance. So glad we did, seeing the property on a bike (very flat and easy ride) was the highlight of that tour as was the Petite and Grand Trianon that are easier to get to on bike (I think we liked that more then the actual palace)
If your son is into tech, like my daughter, she loved working the audio devise at the Louve. It made her feel in control in a museum that is very overwhelming. I made a list of the works we wanted to see before and she was able to work the devise and lead me as we walked around. I think she liked that better then guided tours. Also we enjoyed the crepe making class, we even bought a pan when we returned home and used the crepe and galette recipe we were given that day.