Windows 7 - Cloned partition onto 2nd disk (in same machine) won't boot

Notes: using a MacBook Pro 2011, UEFI and GTP.

1. Replaced the DVD drive in my laptop with an SSD (disk 2).

2. Installed Win7 onto the new SSD, which worked fine.

3. Decided to clone Win7 from disk 1 onto disk 2 as it was a royal pain trying to migrate software over to a fresh install.

4. Clonezilla was used to clone the windows partition on disk 1 to disk 2.

Note that both disks have a windows reserved boot partition (as I installed Win7 on disk 2).

I assumed that EFI boot would be able to run Win7 on disk 2, but when selecting Win7 EFI boot when computer starts, all that came up after was a black screen with one line of random white characters.

I then edited the boot options for Win7 on disk 1 so it would show an option to boot Win7 on disk 2. This works up to the login screen, after logging in, Win7 on disk 2 just hangs on the loading screen.

Any ideas how to make this work? Why is Win7 on disk 2 hanging on the login screen when I manage to get it to boot?

The Windows system disk cannot always be cloned and restored on different drives, since Windows keeps references to disk-numbers in the registry, so that you are unlikely to find all the places in disk1 that need to be fixed.

The normal procedure for such cases is to repair the Windows installation that you wish to boot from. Here are two repair options that should fix disk1 without loosing any installed applications (if nothing goes wrong) :

Startup Repair (might be enough by itself)
Repair Install

After Windows boots correctly from disk1, you can then add disk2 as an additional boot option.

I have done this once before (moving main install to an SSD)

What happens is the BOOTMGR that windows uses in UEFI looks at a parition's identifier when trying to boot, and the identifer got changed when you cloned the disk.

You will need to boot from a disk, and then use bcdedit from the command line to set the correct identifier.

Annoyingly, I have no way to simulate the situation, so I cannot produce step-by-step instructions and/or screenshots.

Just remember to back up your BCD store first!

(Looking a bcdedit's inbuilt help might be of use)

EDIT: I noticed you were on a mac, hold C while booting to boot from cd, and be ready for the "Press any key to boot from cd"

first, Clone everything (include all partitions, EFI, MSR, whatever) from disk1 to disk2.

open the case and take away disk1, put disk2 into disk1 slot.

Boot it up, check if everything fine, if it read recovery, just let it happen.

after everything settle.

plug back disk 2 and then go format it for alternative use.