I find it really odd that ‘06 FJR owners (new or existing ones) are given different answers in the US. I am not sure if state laws play into that, but NHTSA recalls are a must to fix - as I understand. I may be wrong, but this is what my experience was with the my bike’s recalls:
I live in California, and bought my ‘06 a little over two years ago with 7K miles on it, locally. It is a CA model. The ignition recall was done on the bike, and to two keys came with the bike. So, I can’t speak to that recall. The grounding harness issue was outstanding though. I was told by the Yamaha support rep to not to ride the bike, and have an authorized service department complete the recall before I do ride it. Of course, the part was on backorder and - during COVID - there was no expected availability given. After waiting for months I found a “new old part” on EBay in original packaging, and got it. I called my local service, and they installed it for no charge, but no reimbursement was given either. BTW, I did ride the bike while waiting for the part.
Yamaha and the service department declined to fix the the “Tech Bulletin” issues, which was the altitude sickness, and the 37 mpg readout issue. They said that the duration for fixing those issues have expired.