Just a thank you for the pointers on this.
Had to book an appointment, a total of 4 people involved to make everything happen and 2.5 hours spent doing so but all is well in the end.
For the record I did need to show passport + gaijin card. I chose to pay for the 3000odd Yens for the onsite setup and given how long this all took didn’t regret it.
by TokyoBaguette