All cars have problems.
Since you're a previous honda owner, hondas generally tend to be the best built japanese cars you can buy. But even their civic Sir (the ugly one) has problems. interior rattles, funny engine noises.
Mazda has their clunk, and probally very minor interior rattles, well it was for their P5 when I Test drove one.
My Spec V has some problems as well, usually all related to cold temps, my suspenion whines (which is the HLSD) when it's like really cold and I Didn't give it a chance to warm up.
I have some minor rattles, but dynamat seems to stop those, and there are evendly two settings on my sunroof to be opened, one which it stops sliding open at 80-90% to reduce wind noise, then hold it down again it opens to 100% but over like 40KM/h you get crazy wind noise, which I find can be aliviated by opening a window a crack.
I'm not sure how bad this "clunk" is but it'll probally (not) be fixed for the 2003.5s.
you paid what 30K (canadian) for your car? I paid like 23K (canadian) I paid in full, so I don't have an option to drop the lease or anything like that, but if it annoys you enough, just go to the dealership, you're supposed to have a bumper to bumper warrenty.