Can't boot from clone drive

You must do this in order to boot from an external drive:

Boot Using OPTION key:

1. Restart the computer.

2. Immediately after the chime press and hold down the

"OPTION" key.

3. Release the key when the boot manager appears.

4. Select the external disk icon.

5. Click on the arrow button below the icon.

Then I would say the problem is that you cloned a non-functioning system to the external drive where it still doesn't function. You may have a useful backup, but not a bootable system.

What about your Recovery HD? Did you clone one to the external drive? CCC does not perform that automatically. You must do it manually.

Then boot from the Recovery HD on the external drive after you have installed the new drive in the computer.

Install Lion/Mountain Lion on a New HDD/SDD

Be sure you backup your files to an external drive or second internal drive because the following procedure will remove everything from the hard drive.

Boot to the Internet Recovery HD:

Restart the computer and after the chime press and hold down the COMMAND-R keys until the Utilities main menu appears on the screen.

Partition and Format the hard drive:

1. Select Disk Utility from the main menu and click on the Continue button.

2. After DU loads select your new internal hard drive (this is the entry with the mfgr.'s ID and size) from the left side list. Click on the Partition tab in the DU main window.

3. Under the Volume Scheme heading set the number of partitions from the drop down menu to one. Click on the Options button, set the partition scheme to GUID then click on the OK button. Set the format type to Mac OS Extended (Journaled.) Click on the Partition button and wait until the process has completed. Quit DU and return to the main menu.

Reinstall Lion/Mountain Lion: Select Reinstall Lion/Mountain Lion and click on the Install button. Be sure to select the correct drive to use if you have more than one.

Note: You will need an active Internet connection. I suggest using Ethernet if possible because it is three times faster than wireless.

your clone should be from before the problem arised, and of course try using it.

USB2 and Firewire are bootable, eSATA controllers are harder to find.

I had one of my internal SATA ports seem to stop working when I woke the system everything thing looked normal but nothing would run.

I got a "slash" on startup. Could not see the drive and booting was slow from any drive, as well as taking abnormal very long wait to get Option menu to show. Pulled the drive and I could boot off cloned systems. And could restore the system from a known good system.

It is not clear but sounds like you tried to clone a failing system. Maybe I am wrong. And even when repaired best to only recover files not backed up that are essential and not take a chance.

Doing a clean install and using Setup and TimeMachine would be safe if you dont' have corrupt files in backups.

A 'system only' is generally less than 100GB. All the data being on another drive. And make a small partition on other drives.

A PCIe SSD controller can hold two SSDs and for many users allow booting, freeing up one of the internal drive bays.

Cloning even when everything is done right would once in awhile not work. But having Lion and having a Recovery partition on multiple drives should give you enough of a safety net.

Having a non-bootable system though can affect everything else, the system has to - during early bootstrap - goes out and looks at all drives for systems and not just the one selected. Pull the faulty drive and put that in external Docking station or something and put the clone in one of the drive bays. Spare sleds go for ~$20 each if you want a couple, a USB3/eSATA Dock $40.

Doesn't matter if I boot in recovery mode or while holding down option.

Then you are not correctly Alt/Option booting.

The code for Alt/Option Boot is all in ROM, and it should draw a blue of gray screen (the Apple is not present because it is loaded off a drive), then in slow motion, draw an icon for every potentially bootable Volume. Only after you tell it to proceed will you possibly see the gray Apple.

If you are trying to say that what happens AFTER you Alt/Option Boot, then choose a Recovery_HD or a System, is the same regardless of what you choose -- then you need to be much more precise in your descriptions. We cannot see your Mac and MUST take what you say extremely literally.

What model Mac Pro is this? or What speed processor and year?

How many different "Recovery_HD" do you see when you Alt/Option Boot? (Results should be different fro each one.) Do you also have a Time Machine backup drive? It has its own Recovery_HD after 10.7.4, and it will give different results as well.