The UK one is stamped along that top water drainage closing edge for the hood. As well, the UK was stamped into a plate and located in the engine bay. And the Jap one stamped into the boot floor. It's like an Easter egg hunt. 

Ding ding ding, we got a winner. In the boot, just like you said. Stamped into the floor where you mentioned. Thanks. Had to brush away the dirt and such. Have a little bit of rust forming across it too. But alas, the mystery is solved. Wonder why they chose that area? Maybe 'cause the front end rots away so easily, and needs more replacement panels more often. But the boot floor isn't much better. 
The UK VIN was stamped into a maker's plate and attached in the engine bay. Would have been good have them stamp theirs on a plate as well. 
Weird to have two VINs. Hope it isn't an issue getting it registered. 
Thanks folks for your input.

Hi In my past learning on the JDM cars, I've seen the 99X number stamped into the right rear boot floor, just about between the edge of that battery box and the opened boot lid. Occasionally, I've seen that area has that number "Framed" in an area of either abraded away paint or something like that. If you need to get some additional clarity, be sure to check in with some of the VMC members. Best, MSH

I would say it should be on the hood closing panel/ledge. Maybe ask the seller where the plate  really is. I'm sure there are other JDM Minis in Vancouver. The Vancouver Mini Club might know the answer.

Thanks. I cannot seem to find the Japanese VIN anywhere on the car, other than a label-maker label with it stuck on the dash. Maybe I'm not looking in the right spot. Where would it usually be? Would it be stamped in there someplace?

Not sure how it works there in Canada, but here in the US you have to bring the vehicle in for a VIN verification and THEY tell you what the VIN is.  Heaven forbid ... at least here in California... if you have documents from Japan and that you then try and use a number different than what the documents show.

Hello folks. May need a little help with this one. 
My Mini is a Jap import. There are two VIN's on it. One I understand is a UK one that starts with SAXX..., and the other is the Jap 'version' that starts with 99XA...
Which one of these do I use to register the vehicle? The import docs use the Jap version. Do I continue with that?
Figured someone else on here would have had the same issue by now?
I'm also in BC Canada. Not sure if that makes a difference. 
Thanks in advance