In the past we have left our boat in Oz for a period of months under "customs control". This meant that we could use the boat or store it, but not move it from the area of jurisdiction, which in our case was Brisbane
Harbour. The time under customs control was not included in the allowed time "in country". No worries... but be aware that Customs changes the rules more often than they change their underwear, and in fact individual officers have very different interpretations of extant rules. And, the individual officers have considerable flexibility to make arrangements in specific situations.
So, my advice is to contact the office in the area where you propose to leave the boat and sound them out. If they come up with a useable plan, get it in writing!
And as to your being a Kiwi -- you do get special treatment from Immigration, but not from Customs.
Cheers and good luck!