Chosen Solution
I am upgrading my HDD on my 2011 Macbook pro, with a 750Gb Toshiba MK7559GSXP I used CCC and SD to clone the drive , the cloning process finish with out any flaws, afterwards I tested the Clone HDD by restarting the computer and pressing the option and booting from the Clone HDD, it work fine, I proceed it to install the HDD on my 13" Macbook pro, I restarted the computer and after 60 seconds all I get is the Flashing folder with the question mark, I remove the HDD and install the old HDD and boots fine.
This is odd. If you booted from the HD while it was connected externally, it should boot just fine when installed inside of the machine. Re-install the cloned HD and make sure the SATA connector is properly seated and that you are not crimping the fragile cable in any way.
Format the drive before you start (Mac GUID) give it one partition. This is not required when booting from an external.
