I just think you will exhaust yourself with some of your days and might not be able to get it all done. The drive from AKL-Waitomo is closer to 3 hours and the drive from Waitomo to Matamata is at least 1.5 hrs....ZQN to Milford is at least 4.5 hours.....pretty much add 20% to any drive time you see on google maps. The day from AKL-ROT is possible in theory, but you will be rushed and it is very long. I would take out the glow worms as it is a really long way to go to see one thing. Just go straight to Matamata, then to Rotorua.
For option 1, it looks like you plan on taking a rental car on the ferry, right? You need to check to see what the fee for that will be, it is my understanding the rental car companies will charge you heavily for that. I always have clients drop the car in WLG then pick a new one up on the other side.