I'm not sure about the bus and train travel but October is defintily a nice time to go, you will find the south island rather cool though. Allow around 10 - 14days to see both islands. Spots you much visit are Rotorua, Wellington, Christchurch, Dunedin, Queenstown. Akaroa is a nice day trip from Christchurch, and Arrowtown a day trip from Queenstown also.
Your best bet for flying from Queenstown to Auckland is with AirNewZealand, just check out their website.
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