Start with the simple first; glazed clutch pads. It's very common with the 400 and produces jitters, shakes and squeals. Solution, sand down the clutch pads and blow out expended clutch material (ie dust). My local shop charges $40 and it takes an hour, if you're not mechanically inclined. Afterwards, it will run silky smooth once more. Mine usually needs this every 5k-10k miles, but I ride the 400 mostly in heavy traffic.
It could be belts and rollers too. When was the last time they were changed? My experience is to change them every 20k miles. If you're within this limit, you're probably okay.
The smell problem is a bit disconcerting. The pad glazing can produce a burning smell if there are a lot of prolonged starts in quick succession, like riding in traffic or starting off uphill. The secret to riding the 400 is to blip the throttle to 4500 rpm at take off and get the clutch engaged immediately, then moderate your speed. You don't want slow starts as this heats up the clutch pads and produces the glaze that needs to be removed.
Also, this is something the dealer easily could have missed because you have to remove the clutch bell & housing to get to it, a minor job, but one not usually done with a simple inspection.
Good luck. Let us know how it goes.