Sounds like a wonderful trip! Your DS is super lucky!
I would look closely at the terms and conditions for the train pass. The Indian Pacific and the Ghan are both on my wishlist, but they are just too expensive

The cheapest Aussies can do the Indian Pacific Sydney to Perth is about $900 each just for a seat

I'd also like to point out (in case you aren't aware already) that the Indian Pacific takes 3 nights to get from Sydney to Perth.
The Ghan takes one night Adelaide to Alice Springs, then one more night from Alice Springs to Darwin. Once in Alice Springs, Uluru is still a couple of hours drive away. On a positive note, June is a pretty perfect time of year to visit the red centre.
DH and I did the Sunlander last year and we really enjoyed it. However, I believe it has been discontinued and replaced with the 'tilt train' which doesn't have any cabins, but I believe you can get a 'lie flat' business class type seat. It runs overnight from Brisbane to Cairns and I believe it takes about 25 hours.
Other train journeys within Australia are just a means to an end, and can be an inefficient use of time. They are not high speed like the European ones (which I think are fantastic too!). For example, it takes about an hour to fly between Sydney and Melbourne, but it takes about 12 hours on the train. If you really enjoy train travel though, and find yourself with plenty of time to get around, by all means do it
I would recommend flying between the major cities in your itinerary, and maybe hiring a car for excursions from the cities (like Great Ocean Road and Philip Island from Melbourne). Driving on the 'wrong' side of the road can be a little nerve-wracking, and I found it required a lot more concentration than I usually had to use while driving, so I fatigued a lot quicker. For this reason, be sure to schedule lots of breaks and driver swaps if possible for any long road trips.
What were you thinking of doing in Perth? I grew up there and can definitely help you out with that. Fremantle is good for history, there's the Swan Valley wine region not far away, and of course plenty of great beaches (although it will probably be too cold for swimming)! Rottnest Island is also an interesting side trip if you've got time, a short ferry ride from Fremantle, car free (hire a bike to get around), and the only place in the world where you will find the cute little marsupials called Quokkas. Be aware that places like Margaret River and Kalbarri are a long drive from Perth on (for the most part) very boring roads!
Have you thought about including Tasmania in your itinerary? It will be cold down there at that time of year, but I think it's one of the most spectacular places for scenery in Australia. Also a lot of history if that's your thing.