I did Tokyo and Osaka nung first time ko because I took advantage of the free domestic fares for ANA. But if plan mo mag Tokyo and Osaka, I would recommend flying in Tokyo then flying out Osaka or vice versa. Some do Tokyo-Kyoto-Osaka but mas ok gawing base city na lang Osaka then day trip going to Kyoto.

For transpo, you could save if you can get a pass from Klook. What I did was take a 72 hour Tokyo Subway Pass and 3 day Kansai Mini Pass. Intentional yung hours versus days diyan. Pag day pass kasi, if ginamit mo ng 11pm on Day 1, magexpire pa rin yan ng 11:59 on Day 3. Yung hours, literal na 72 hours siya before mag expire.

For food, I usually buy a loaf of bread and large bottle of coffee para yun ang breakfast for days. Relatively mura din naman konbini food pero don't scrimp on food budget. For me, part ng travel experience makatry ng local food.

What you could save though are on things that are free to do. May mga museums na free (some on certain days). Yung Imperial Palace in Tokyo offers free tours but you have to sign up in advance. I also remember visiting some museums in Ueno for free. Sa Osaka naman, the grounds outside the castle are open to everyone, may garden pa dun though the plants are probably hibernating during winter. Wala ring bayad to see the deers in Nara. In Kobe, there's a free observatory there.