I'm only resurrecting this thread because I followed the link that a newbie, PatMitchell, was provided that asked "what is the SH-46" code? and I landed here. Like Jasen, I had been mostly absent from the forum for a couple of years. In and out on occasion but I lost track of a lot of you peeps. I hated to read the troubles and turmoil Jasen went through. I hope you are now back on solid ground and I presume you are still riding the '07AE.
Although Jasen's bike was getting the SH_46 code, the conclusion seemed to be that the problem may or may not have been clutch related. But The answer to the new guy's question is in this thread.
SH_46 is indeed the the shift error code AND you ARE going to need a new clutch, sooner rather than later. I think mactrophy and others clarified that, but it was somewhat buried in and among Jasen's various posts with his diagnostics of his specific problem.
I had the SH-46 Shift error code about four years ago that started around 35K and gradually got worse over the next 10K, to the point I just about couldn't even ride in 5th gear. I had bitched to my dealer a couple of times in the interim and nothing was ever done. Until one day, with wifey on pillion, returning home from the GA mnts., raging down GA 400 in five or six packed lanes running 70+ when all of the sudden 5th gear had no pull and SH_46 popped up, with me in the far left lane, thin strip of pavement between white line and jersey wall. OH SH*T! I managed to work it over and get out of the danger, but it was a BAD scene. After limping the bike back 150 miles to Birmingham I dropped it off the next day at my local dealer and gave them a damn earful about how they almost got both me and my wife killed by not replacing the clutch that I had been telling them for six months was going out. Well, there was no question is was going out now. It was repaired under my Y.E.S. warranty. I just passed the 100K mark and I have recently begun to feel the occasional chatter in cold, first gear, heavy load starts, which is exactly how it started the first time. I imagine I'll begin feeling some slippage in the next 5K. Then the first SH_46 code will pop and I'll install a clutch. Since Jasen's six year old son did his, I am obliged to do my own now.
AND, because she's not covered under the Y.E.S. any longer...
Long story short, SH_46 = new clutch sooner rather than later. I recommend sooner so that you don't find yourself in a very dangerous situation like I did four years ago. Good luck!
Oh, and BTW, I hope you have since washed that dirty azz bike Jasen!