I'm not understanding why "gross sales include GST up until August?" If you were not registered for GST, you should not have been charging GST on your invoices. In my humble opinion, I would suggest that you strip all of the GST you have collected, and separate the GST from the expenses, and remit the difference. I suspect that you are likely to be an annual filer for GST so it should look more reasonable.
In order to regularize your invoices, you can forward a copy of your first invoice, showing that you were adding GST to the invoice, and they will happily back-date your registration.
