There is so much to see on this planet......

A few ideas:
When you are in SCL you should consider going to Easter Island. One of my favoured places in SA. And/or Macchu Pitchu. Easter Island you can to from/to SLC on LAN, MP: Take LAN to LIM and buy an extra ticket from there to Cuzco. LIM is not terrible safe - as most of South America, but you should not be too worried.

SYD is great, but everything else is too far for driving. You should consider flying to Cairns and/or Hobart or Uluru (Ayers Rock).

Also travel in China is cheap, you can always buy seperate tickets there. Try www.zuji.com from HKG or www.elong.com inside China. Xian and Shanghai are two places i would look into.
HKG is one of my favored places, PEK is a bit boring.
If you need some more ideas in Asia look into Vietnam, Cambodia (Angkor What), Laos (Luang Prabang) or even better North Korea (most memorable trip for me in the last few years).

SIN-BKK: CX is flying that route if you don't want to take the train.

I personally are not too crazy about JNB - never feel safe there. CPT is ok, you could take the car up into Namibia (or buy a seperate ticket to Windhoek and go up to Etosha and west to Swakopmund.Nice and safe.