Are you using etax? Because I think it would answer most of your questions or automatically work them out for you.
What I can answer from the list -
Income is anything either from a job, interest or rental, etc - so CCR is not taxable as it is a refund of half of what you've already paid out.
Parental leave would be included with any group certificate received from that position as it is still income
Yes to the medicare levy surcharge - again that should be automatically caluclated by etax.