Just to help you in the futurr, for partner awards, the operating airline has their own confirmation code for your PNR that is different than Alaska's. Some partners you have to call to get that info after the award is ticketed.

Let us know how it goes. Probably not much that AS can do, especially since it wasn't on their own metal and they had to compensate JAL for the seat that couldn't be sold. But not getting a confirmation email for the award being issued is strange.