MacBook Pro 13" Only boots to safe mode and running VERY slow.

Hi...
Not posted on here before, but am desperate so hoping there are some experts out there who can help...
I have 13" Macbook pro which has ceased to work properly - it runs very slowly and will only boot in safe mode.
I have installed a new hard disk, but I get the same problem whether I (try to) boot from the old HHD or the new one.
The new drive was imaged using Carbon Copy Cloner.
I have run the repair disk priorities in disk utility and verifying the disk says all OK.
I have set the startup disk to be the new hard disk, and cleared the NVRAM via cmd-option-p-r...
As things stand at the moment, rebooting (not in safe mode) leaves me with the grey screen and apple logo (and no obvious activity for 10+ mins (so far)).
Booting in safe mode takes 3+ mins but I do get to a user login prompt and can get to a desktop.
Any ideas / help very much appreciated as I urgently need to get this machine working!
Thanks!

Domonic White,
when you ran Disk Utility, did you do so from your user account, or from Recovery mode? There are four options there: Verify Disk Permissions, Repair Disk Permissions, Verify Disk, and Repair Disk. Which of these did you do in Disk Utility?
Have you tried resetting your MacBook Pro’s System Management Controller?
Have you tried logging in as your administrative user, opening the Users & Groups pane of System Preferences, creating a new standard user (e.g. “Test”), and trying to log in as the new user, to see if the slow performance affects the new user also?
There is a chance that this could be due to a faulty internal SATA cable. If you have an external disk enclosure, or a SATA-to-USB or SATA-to-FireWire adapter, try booting from one of your drives when it’s externally connected. If it works fine that way, but is sluggish when internal, that could point to your internal SATA cable as the culprit.

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