Does the price of this pass include the Hakone ropeway and boat ride on Lake Ashi or is this a separate cost?The sightseeing boats are included. But only one of two boat companies.
Also is there a cost involved to enter into pavillions and temples throughout Japan?
Major temples charge an admission fee of typically 200-1000 yen. The average is around 200 yen in Kamakura. Around 500 yen in Kyoto.
I am not sure what you mean with "pavilions".