First, you need to do this:
Repairing the Hard Drive and Permissions
Boot from your OS X Installer disc. After the installer loads select your language and click on the Continue button. When the menu bar appears select Disk Utility from the Utilities menu. After DU loads select your hard drive entry (mfgr.'s ID and drive size) from the the left side list. In the DU status area you will see an entry for the S.M.A.R.T. status of the hard drive. If it does not say "Verified" then the hard drive is failing or failed. (SMART status is not reported on external Firewire or USB drives.) If the drive is "Verified" then select your OS X volume from the list on the left (sub-entry below the drive entry,) click on the First Aid tab, then click on the Repair Disk button. If DU reports any errors that have been fixed, then re-run Repair Disk until no errors are reported. If no errors are reported click on the Repair Permissions button. Wait until the operation completes, then quit DU and return to the installer. Now restart normally.
If DU reports errors it cannot fix, then you will need Disk Warrior and/or Tech Tool Pro to repair the drive. If you don't have either of them or if neither of them can fix the drive, then you will need to reformat the drive and reinstall OS X.
Second, clone your drive to a freshly formatted external drive.
Clone using Restore Option of Disk Utility
1. Open Disk Utility from the Utilities folder.
2. Select the
destination volume from the left side list.
3. Click on the Erase tab in the DU main window. Set the format type to Mac OS Extended (journaled, if available) and click on the Erase button. This step can be skipped if the destination has already been freshly erased.
4. Click on the Restore tab in the DU main window.
5. Select the
destination volume from the left side list and drag it to the Destination entry field.
6. Select the
source volume from the left side list and drag it to the Source entry field.
7. Double-check you got it right, then click on the Restore button.
Destination means the external drive.
Source means the internal startup drive.
Now, you can use other cloning software but the most reliable and easiest method is what I've described above.