If the file structure is bad DO NOT USE CARBON COPY CLONER. It clones drives on a block by block basis (I have it running right now, actually), and it will copy the structure problem to the new drive. If it's a mechanical problem to begin with, then you should be able to fix the structure with Disk Warrior, but still, why create more problems?
I suggest doing a clean OSX install on a new drive, then choose to shut down when it says it will restart (do a hard restart if you need, hold down the power button until you hear the drive spin down/roughly 5-10 seconds), reconnect the drive (no need to pull it entirely, just disconnect the SATA and power cables before you start the install and reconnect them at this stage) before booting into the new drive, and during the registration pages just import your account from the old drive. Provided there is no corruption at the user folder level, you should be able to get all your settings and apps and everything onto the new drive without a problem. Then just run disk utility, repair disk permissions, and you're ready to start running software update (ALWAYS run disk utility after each update; run software update, restart, run disk utility, repeat, until you're done). I did that earlier today on a G4, only took about half an hour.
Good luck!
EDIT: just saw your last post. Follow the instructions above and you should get exactly what you're asking for. But as another user said, back up your essential files ASAP, burn them to DVD or copy to an external drive or something, you don't want to lose anything irreplaceable. It would suck to lose your itunes library or web browsing settings, but not nearly as much as your financial records or family photos and the like...