Hope your problem is something simple but there have been some problems with early AE shifting components. There was a recall for some of the early Gen II AEs because of a faulty actuator rod bracket. When it fails it will cause a SH 51 error code. There is a good chance that your '06 was part of the recall program. Once you hook up with a dealer they will be able to tell from your VIN if your FJR is in the recall range and if the recall work has already been done.
You can remove the left side cover and inspect the shift actuator to see if it looks displaced. The rod will be attached to the mount, but the mount won't be attached to anything. You can manually move the rod to shift the engine for emergency maneuvering.
The fix is a new, stronger bracket. A dealer would 1) have to have a bracket in stock 2) be willing to call other dealers to see who may have one in stock 3) take a bracket off an AE on the floor and put it on your bike, then replace the bracket on the donor bike when one comes in.
Good luck! Since there was no description of your failure I hope that I'm off base with my guess.