We did almost this same trip in November. We didn’t have a rail pass. We flew into Narita and back from Osaka so had one bullet train trip costing just over £100 each. Travel in Tokyo all by subway with Suica card that we topped up as we went along. Spent about 5000 yen in all on the card which we used in Tokyo and Kyoto subways and buses. We travelled in Kyoto by bus or subway, neither expensive. All bus journeys in Kyoto were 230yen however far you went so very cheap. We did day trips to Mount Takao from Tokyo and Nara from Kyoto but these were not expensive so it was definitely cheaper without the pass.
Incidentally Mount Takao was a great inexpensive day trip from Tokyo and we got to see Mt Fuji from the top, as well as see lots of temples on the way.
And we were slightly disappointed with Nara -so so crowded! So many wonderful temples and gardens in Kyoto itself.