I think it looks good, but make sure to leave a lot of it open to change. All over South America, you can take night busses from place to place, though some parts are worth flying to/from, like Colombia to Peru, and within Peru, the Lima-Cusco route. Try not to lock yourself into specific dates and times if you can help it. The best of SA is not necessarily the big cities. For instance, I'd recommend less time in Lima vs. Cusco, and try to work in Bolivia's Uyuni Salt Flats on your way to Buenos Aires; it's some of the most incredible scenery I've seen in my life. The overland journeying in this part of the world is a big part of the whole experience! And inevitably, you'll want to stay longer in one place versus another, so leave your options open.
I agree with dropping the week in Bali, unless the flights work out that way. There's lots to see in SEA and it's easy to get around, so just leave it open and your two months will work itself out. I liked Australia well enough, but for me NZ was a highlight. I did both islands in 3 weeks, but with 5 it would have been a lot more comfortable. You won't run out of things to see.
Honestly, 1 week in Japan is very rushed. Tokyo itself deserves a full week, and Kyoto/Nara at least 2 nights. It'll also be the most expensive part of the trip.
