Those boot will make you much happier. Sport Bike boots aren't too fun to walk in.
I still can't believe the mech dinna open the variator cover. =P Did you mention the grabbiness of the clutch?
As for the suspension, the noise can be anything. I can't imagine you are bottoming out the front end. You WOULD NOTICE that, and the front end on the DT300 seems pretty stout. When do you hear it? Stopping, deceleration, or just bumps?
The wiring inside the cowling is REALLY well done and taped up. I doubt it is a loose wire. Could be the brake line. It is stiff and braided - quite normal.
You could do what I do - Put in some earbuds, and hook into the iPod. That helps protect you from hearing damage, as they muffle the outside sounds. And the music is great.
Haven't heard any weird engine noises - Or really ANY engine noise since using them. HA!