Aaaand success!
I don't know why but the first few times I tried the pokecoupon menu on the left I got the garbled menu screen you see below. Only after a exiting out and getting back in few times did I happen to get the proper menu screen in the middle screenshot. Just select the top option and select yes. I've no idea if it actually charged me any pokecoupons or not but it saved a pikachu to the empty slot in my party.
A point of interest, after saving, it also came up with another yes/no option but I have no idea what I was choosing yes or no for. I selected no and it sent me back to the garbled menu. I also tried the second option (I can't read Japanese so I've no idea what it says, other than there's GBA in there) but it actually made the emulator throw up an error so not sure what that or any of the other options do.
Anyway, hopefully someone will gain something from my hours of frustration. AR codes and your own US or PAL disc are all you need. By all accounts the US version is no where near as buggy, with actual translated text so if that's your version you may have an even easier time with the whole process.