I'd scratch Coober Pedy for a first trip unless all 3 of you are really interested in learning about opals, opal mining or have a strong desire to experience a stay in an underground hotel with zero sunlight (hope no one is claustrophobic in your family!). If all you want to do is buy yourself some opal jewelry, you will have tons of opportunities to do that in other places in Australia. It's everywhere!
To be perfectly honest, I found Ayers Rock (Uluru) to be sort of underwhelming. If you have spent any time at all in the American Southwest, seeing this lone giant rock, and even visiting nearby Kata Tjuta, just does not seem quite as spectacular as what we have in our own backyard. A lot of tourists choose to climb Uluru, but this is seen by the Aboriginal population as extremely disrespectful. The best time to see the rock is at sunrise (if you aren't early birds, standing around the cold dark desert waiting for the sun to rise might not be everyone's cup of tea), or sunset.
Also, when you stay overnight in that area, you are basically at the mercy of the corporation that pretty much controls the pricing of all lodging and food. Unless you go ultra, ultra luxe, it's sort of like being trapped at Disney, albeit with far fewer choices. The lodging is just OK, the food extremely mediocre and super overpriced.
I'd skip it and use the time to go to Melbourne and travel the full length of the Great Ocean Road heading up towards Adelaide and then I would suggest time spent on Kangaroo Island which was great. I'd choose that over spending any time in Brisbane. The Australian Zoo was ok for a few hours, and it's great that you have a contact who can give you some behind the scenes time, but it's still a zoo. I find it a lot nicer to see the animals in their natural habitat instead of behind bars. If you just want to hold a koala, you could go to someplace like Featherdale Wildlife Park just outside of Sydney and combine that with a day trip to the Blue Mountains.
I agree with basing in Port Douglas if you are going up to the Great Barrier Reef. Much nicer than Cairns. For Sydney, The Rocks is a good (albeit touristy) location to stay as you are within easy walking distance to the Harbour for the Opera House, Bridge, Botanical Gardens and ferries heading towards other points, including Manly - nice beach, fun and very scenic ferry ride, but I don't know that I would want to stay in Manly and spend that much time on the ferries commuting back and forth between Manly and Sydney. "Old" is sort of a relative term in Australia. Unless you are talking about aboriginal areas, it's still a pretty "new" country - like the US. You might see some quaint victorian type architecture scattered about in certain areas, but it's more 1800s/early 1900s you will see - not like Europe.
If you have not purchased guides yet, check your local library and see which ones you like before you purchase.