Upon landing at Tokyo Narita or Haneda Airport, buy a Suica card at the airport for convenient travels, then take the Narita Express or an airport bus to your accommodation.
Take the Shinkansen (Nozomi) from Tokyo Station to Shin-Osaka Station; the journey takes about 2.5 hours and costs around JPY14000. Purchase a Japan Rail Pass if you plan to return, as this can save you money.
Take the JR Special Rapid service from Osaka Station to Kyoto Station, around 30 minutes, costing JPY560. Using your Suica card can make this journey seamless.