There is a massive "EPA" thread already in the Vic section
http://www.skylinesaustralia.com/forums/topic/156269-the-epa-threadroadworthy-thread/
Go have a read of it mate, read the entire thread.
There is plenty of good info, experiences and so on to learn from.
End of the day, an officer can report you even with a stock exhaust.
So welcome to the club of EPA notices, most people get at least one in their lifetime.