I agree with the advice to choose either Japan or Southeast Asia and stick with it.

Remember that the countries in Asia are all very different and that the distances are greater than you would find traveling between that many countries in Europe.

Your proposed itinerary would give you an "if it's Tuesday, this must be Belgium" feeling.

September can be typhoon season, but if you're in Tokyo, which is partly sheltered by the Boso Peninsula, you will experience a typhoon (if there is one) mostly as heavy rain, and the same would be true of Kyoto, which is inland.