I guess to find the source of what you describe as a missing shortcut could be challenging.

What I would suggest now is that you wipe the HDD after proper backup of all needed data and see how your SSD works then. If it gives you back your fast results, go ahead and set up a new Copy of Windows 7 on the HDD.

If you then have two working operating systems and good speed on SSD you are fine. If your SSD Windows still feels
not just all fine but speed is good in ATTO, also reinstall the OS on your SSD. Then you have two clean systems.

In case things dont work out fine with two parallel operating sytems, keep the OS on your SSD and do regular backups on the HDD or even better on an external storage. If your SSD breaks you can recover your OS to your HDD while waiting for your new SSD.

In case an external harddrive does not work for you create two partitions on your HDD. One to store your backup and one to serve as System partition if the SSD breakes. That system partition should have the size of your SSD.

In any case... have some trust in your SSD it usually doesnt break down half as fast as an HDD. But that can depend on many factors. HTH