I think you'll probably need to scale back expectations with the itinerary - The three days starting with Day trip to Nikko (4+ hours round trip and high intensity day if you want to see more than a couple of sights), Night around Mt. Fuji (2+ hours travel and a change of hotels), Travel to Kyoto (2.5+ hours travel and a change of hotels) seems like a lot of movement and disruption. Your jet-lagged two-year old might not handle this very well. I don't know your two-year old but the two-year olds that I do know would be altogether more amenable to a slower pace - so perhaps you could keep the same list of places to visit but stretch things out..