Thanks for your question. First up, can the master franchisor provide any advice, I would imagine you are in the same situation as their other franchises and that these questions have been asked and answered before?
Sounds like you have done some research already and understand a bit about GST which is great, the IRD does have a lot of information on their website and you can call them and discuss this, for free, http://www.ird.govt.nz/gst/registering-for-gst.
As far as I am aware, you will need an IRD/NZBN number for your business however that doesn’t mean you are GST registered, thats a seperate “form to fill”.
Have I missed out doing so for this financial year?
I assume you mean the 2019/2020 financial year, returns for that period need to be filed before March 31, 2021, so you haven’t missed out on that, you will still be able to claim expenses from that period in your return.
Managing and recording your expenses, the lowest cost way to do this is on a spreadsheet. If you feel competent, setup your business with Xero, its not expensive to do this however you do need to have a bit of financial literacy. This will allow you to significantly reduce any accountants fees later also as you are largely doing all the work and they will simply access your Xero account and prepare accounts. Makes GST filing a ton easier also.
There are guidelines with the IRD about mileage allowances, home office allowances, etc, need to keep an eye on FBT (fringe benefit tax).
All the said, as much as you aren’t keen to spend $’s with an accountant, it probably would be money well spent. You could possibly get a local accountant to provide you with a fixed price quote to provide the advice.
Good luck and I hope your business does well.