Re: the Johannesburg dates not lining up, is it better to book now in the hope they'll release more Classic Reward flights for a more suitable date and then pay the 5k points to reschedule?
You
can book the 1st leg now - it'll mean that the entire itinerary will be priced / re-priced in AUD for the taxes (rather than in ZAR where depending on the credit card you use, might incur international transaction fees).
If you're able to see new reward seats on the dates you prefer after you've booked, you will then need to get over the hurdle of getting through to someone who can see and change your flights accordingly. If you don't have high status (ie. Platinum), this will be a difficult task.
You may be able to see seats showing online, but a lot of consultants won't be able to or they'll make up some excuse that seats showing online are for new bookings only / can't be used towards existing ones.
From there, if you're able to add / change legs, you'll need even more luck to get the entire itinerary re-ticketed with a new e-ticket number and within a reasonably quick timeframe.
Not trying to scare you off, but there's a risk of changing these sorts of itineraries with multiple legs with partner airlines as the partner airlines require Qantas to re-ticket any changes etc.
You'll have to be very alert and follow-up with Qantas once / if your legs are changed after the initial booking to ensure you get a new e-ticket issued (normally the Qantas PDF file).
It's best if you can find alternatives now / be flexible with dates etc, to get your booking done in the one go - long story short, try to do as much as you can now, without getting any phone consultants involved.