Is it a 2006 thing????
I also have a 2006 from new, now 45k miles on it. I've never been impressed with how it shifts. This with all the talk here of how smooth The ST1300 shifts. I've cleaned and lubed the ball joints in the linkage, (You know you can adjust that linkage to set shift lever height right? This could help.) Clutch is always clean and bled, Tried different oils, etc.
I even had 2 shops test drive it 3 times under warranty and they said no problems. I don't think they wanted to rip the bike apart.
I also feel the distinct 2 step notch when I shift. I think it's shift fork or gear dog related. Mine will also "get lost" between shifts occasionally. Not a false neutral but the lever goes dead. It won't grab the next gear without first unloading the power.
I also feel I shouldn't need to be concentrating on shift technique all the time. although when I don't is when I get that dead shifter lever thing.
IGOFAR: On the clutch rebuild which way for the sharp edges? That's a new one for me. Wish I had known this on my last 3 clutch installs.
Iirc the sharp edges should be facing outwards..and you should soak the plates you will use in the oil to be used for a few hours prior to installing them.