Kyll,
1) The flying varies depending what aircraft. A young bloke who is fresh out of 20CU will get around 200 hours in the first year at an operational squadron. Once he (currently no female fast pilots) is C-CAT qualified, the amount of flying will increase.
2) Secondary duties can vary. Navigation officer is pretty common which is making sure all the charts and clearences are ready if your going to go overseas. Just generally making sure everything is organised.
3) When you say Junior Officer, what exactly do you mean? If you mean Pilot Officer or Flying Officer, then yes it does. Remember you are an officer in the RAAF who's job is a pilot.
4) Post wings it depends what aircraft your chosen for. Where you said 2-3 years at each stage is not correct at all. I knew a bloke who went by the callsign 'Tik' and was 22 while flying Hornets out of the 75th. Fast jet training in total takes around 4 years to complete, so you can work it out from there. The timeline for this training is 79 (Pearce)-76(Willy)-2OCU(Willy)- Operational SQN.
Although on the surface each squadron appears to have the same roll, they differ slightly. No 3's main goal is total air dominace with a secondary duty of air to surface, while the 77th is the opposite.