After talking to a fella at EV works about various components I have settled on parts for my bike.
Motor: This is the less complex and slightly more powerful out of the two 48V motors. http://www.evworks.com.au/index.php?product=MOT-MARS-ME0708
Batteries: At the moment I'm getting 11 of these cells and will update later to 16 so I get the full 48V system. These will take about 6 weeks to ship so lots of time to draw up some concepts for attaching them. http://www.evworks.com.au/index.php?product=BAT-LFP60AHA
Controller: This one gives the best acceleration for my price range. http://www.evworks.com.au/index.php?product=CTL-AXE4844
Contactor: Good economical option. http://www.evworks.com.au/index.php?product=REL-ZJW400A
Charger: KP3612EL is not currently stocked so will have to wait for that. The charger will be the only component I will need to replace when changing up to 48V.
Battery Management System: Another component I need to wait for. EV works are developing a new, more compact BMS which should be ready in a couple of weeks.
Braided Cell Interconnectors: http://www.evworks.com.au/index.php?product=BAT-EVW-BCI-60-6
That's all I'm ordering at the moment and these parts, including shipping from Australia to NZ, should cost about NZ$3800 (US$2800). I'll be getting other things like DC-DC converter, gauges, power cable and lugs from an electronics store in NZ once the bike starts to take shape.