I bought my Stone brand new on April 5th, just rolled over 5600 miles on the commute home friday morning, just got the kit in the mail to do my service at 6k. I too smelled the clutch for awhile but it will come to pass, they point it out in the manual as a thing that could happen. The suspension gets better over time too, for me anyway. It started out pretty rough but I've realized I've mostly forgotten about it, the components have broken in or a combination thereof, have yet to adjust the rear or anything. It really isn't that world-endingly bad as a lot of people have made it out to be, I figure if you're a problem looking for a solution than yes you might hone in on the suspension. To date I've put $2-2.5k worth of mods into mine, none of that going towards suspension and I don't regret it one bit, not sure if I ever will honestly.
Keep doing what you're doing, just ride the thing. Mine has yet to miss a beat.