Hi S,
On the 1st point I can comment regarding experience with my IS200 which has now over 100,000 miles on it. I had one of the front balljoints replaced (€90 part)as it was making a popping sound every time the car rolled from left to right (curves, roundabouts) or hit a bump with the right front wheel. I mean, these were fairly loud clonks.
Now it is hard to hear, but I am suspecting a similar thing with one of the joints on the rear stabilizer bar. But it might be something clonking in the boot as well.
Just make sure it is not one of the brake pads that is shifting in the caliper. So the clonk shouldn't coincide with applying the brakes or changing direction (say, from forward to reverse). If it does, it's probably the brake pads that need a new one of those spacer-springy thingies . Or some extra copper ease.
Maybe someone else can comment on your paint job problem ;)
Cheers,
RX-Men-8