Okay, here is what you do:
Go to "tax my vehicle"
Because you don't have a V11 tax reminder, enter the 12 digit reference from the V5. It then told me my vehicle was already taxed but gave me the option to continue, where I was able to self declare MOT exemption. I then "paid" £0 for a fresh years historic vehicle tax starting 1st May
I now need to see how long before it reflects that MOT exempt status at "check my MOT"