I found out what the big clunking metal to metal noise was coming from. Me, like an idiot, when putting on winter tires/wheels put a front one in the rear and a rear one in the front. The collar adapter thing on the inside of the wheel was a mismatch (different for front and rear) and caused the major clunking noises over bumps.

As for the initial minor squeaking, I still don't know where that is coming from and I still hear it. It kinda sounds like 2 porcelain dishes rubbing against each other - not loud but subtle and annoying.

I've already tried pushing down on the strut towers long ago, couldn't generate any noise.

 

visually inspect your convertible top, suspension, sway bars, etc.

 

did you ever figure it out?

I just noticed the same noise coming from the front on my 03 today.

 

I have the same problem and i just bought the some tein flex and thought that would go away and someone said i should loosen the under strut bar im assuming and tighten it but as i look at my bushings they look damaged and deterioated so damn i dont know what to do and honestly its kinda embarrassing to have a cool car and lose all kinds of cool points when going over a bump when it squeeks and have people do that "ooo" face when they here it

 

Almost like YellowS2kPower mentioned...

Try pushing lightly on the hood, but right in the middle.
I often get a squeak while driving over bumps because of the hood latch.

You can sometimes duplicate it by pushing up and down on the hood right over the latch.

Used to drive me nuts because it sounded like it was coming from behind the dash near the radio.

Silicon spray or grease can fix it if that is the cause.