Especially since NRT is not convenient to Tokyo, I would not choose to make a stopover in Tokyo for one night. I would connect straight to BKK in order to have another full day there to relax and enjoy the city. You can have all of the good meals you need in Thailand, so I think Tokyo is best saved for another trip when you can spend at least several days here.

Also, I would suggest spending less time in CM in order to have more time in Phuket or Krabi. No more than three nights in CM should be sufficient.

Also- I would fly directly (or with a connection) from CNX to Krabi or Phuket at once- there is no need to spend a day in BK as a stopover. There is one direct flight per day on TG from CNX to HKT- for Krabi you would have to connect in BKK.