JR Rail Pass isn't always worth it - put your itinery through here to check:
https://www.japan-guide.com/railpass/
I returned from two weeks in Japan last Sunday, for anyone thinking of going but wondering about costs we (me and my partner) spent £4091 between us for 14 days in Tokyo, Nagoya, Kyoto, Osaka (incl day trips to Kobe and Nara) and back to Tokyo again.
Parking at Heathrow: £143
Flights: £634.40 for me via Frankfurt with Lufthansa/ANA, return via Zurich with Swiss; £699 for my partner with China Eastern as they went back to China for a week before I arrived in Tokyo and we met up on the same day.
Accommodation: £943 which was mostly using business hotels (APA, Sotetsu Fresa, and a great one called Lamplight Books in Nagoya) but also a normal Japanese house in Kyoto for two nights.
Travel (Shinkansen): £60~ for the Narita Express, £123.49 from Tokyo to Nagoya and then £209.03 returning from Osaka to Tokyo - everywhere else was with our Suica cards which we kept topping up with 3000 yen as needed.
Cash (food, excursions, etc): £1392 in total which was mostly food (snacks from supermarkets) and eating out as well as gifts to bring back (incl £40 worth of KitKats). Excursions (not including temples and places open to the public) included the Mori Tower, Sumida Aquarium, Nagoya Science Museum, Nagoya Castle, Kyoto Railway Museum, Kyoto Tower, Monkey Park in Arashiyama, Osaka Aquarium, Mt Rokko Cable Car, and a meal at Mouriya in Kobe for the best steak I've ever eaten.
We withdrew £1048 in total over the two weeks, but to be honest the places that only took cash were in the minority so we could have used the card for more of that. We spent about £10 a day just buying snacks for breakfast in the hotel rooms tbh which we didn't need to but my partner isn't an early bird.
I paid £22 for a sim card with unlimited data and we used that as a hotspot everywhere we went, but all of the hotels also had free wifi and free wifi was available everywhere.
I'm already planning another trip to visit the north and south of the country in a couple of years, and I'm happily paying extra for direct flights but otherwise a similar budget.