The route will go up from Melbourne along a path similar to the existing Countrylink line and the Hume Highway, passing through Albury, Wagga Wagga, Canberra. From Canberra, it will either follow the Hume Highway or diverge via Wollongong and the coast, on its way to Sydney. From Sydney, the line will follow a fairly straight line to Newcastle, whence it will go either along the coast or slightly inland, with a recommended route taking in the Gold Coast on the way to Brisbane. The journey will take one hour between Sydney and Canberra, 1:50 between Canberra and Melbourne, and 3 hours between Sydney and Brisbane. Journeys are expected to cost between AUD99 and AUD197 for Melbourne-Sydney (in 2011 dollars) or slightly less for Sydney-Brisbane.
As far as stations go, some likely sites have been identified. In Sydney, the obvious one is Central, though pressure from wealthy NIMBYs in the northern suburbs may necessitate moving the terminus to Parramatta (which, despite being talked up as "Sydney's second CBD", would negate some of the advantage that high-speed rail has over air travel, i.e., directly connecting city centres). In Melbourne, the trains would either terminate at Southern Cross or at a new terminus in North Melbourne, with Southern Cross looking better. In Brisbane, the likely terminus is Roma St., whereas in Canberra, there is likely to be a through station, either in the centre or by the airport. For what it's worth, the report assumes that the system would be built to European specifications, and consist of trains running at 350km/h on lines capable of a theoretical maximum of 400km/h.
For what it's worth, there is a history of Australian high-speed rail proposals here. So far, no true high-speed services have been built in Australia, though systems linking the eastern capitals have been proposed in the past. The current proposal was commissioned by the Labor minority government, under pressure from their Green coalition partners, though now has nominally bipartisan support.