Disclaimer - I live in Singapore and have been in Japan/HK/Bali/Thailand/Vietnam multiple of times.

If you decide to go to Bali, avoid Kuta - it is full of drunk, loud, tattooed westerners (read - Australians) and has very little to do neither with relaxing atmosphere nor with authentic Bali culture/history. If you want both, recommend to stay in Ubud.

Please consider that 5 full days (or more) will be spent just to get from hotel in country A to a hotel in country B. With associated tiredness. Not the best option if you ask me.

On a separate note - if I had a choice (and budget) I would stay in Japan for whole time and buy JR Pass to get from place to place. I would not recommend mixing Japan with SEA - two completely different words, culture and experience.