You don't mention if she's a brand new bike or if you've put 680 on a used bike. Regardless you shouldn't experience bad clutch judder, if any at all. These girls have a massive clutch pack, to handle the torque, but are super smooth in my experience.
I've no experience with hill hold. Old school right foot hill hold for me.
Slight wobble on deceleration. Under front brakes or just when rolling off throttle? If brakes, you may have a warped disc. Other causes would be poor wheel balance, which would be noticed under normal riding anyway, or badly worn tyre, Mal adjusted steering head bearings.
Notchy gears. My girl slips into first like butter. Barely noticeable compared with some other bikes. I use TSA for all other shifts and depending on revs get some minor clunks but not what I would call notchy. I suspect that your notchy gears have something to do with your clutch judder.
Take her to your dealer and don't take their brush offs. Take a demonstrator for a ride and compare.