Not booting after replacing the SuperDrive with SSD I am having trouble after replacing my iMac's SuperDrive with a Solid State Drive (SSD).

I kept the original Hard Disk Drive (HDD) in place. I configured the SDD as the main startup disk and I transferred all the libraries in HDD.

The malfunction is that in the process of rebooting the iMac turns off.

Booting into safe mode the Disk Utility shows the new SSD drive is full, although before rebooting it has used only 90GB out of 480GB. I do the same procedure again, clean install of macOS 10.12, and again the same problem. Any ideas please for solution of this malfunction?

I have to say that if I do not reboot the iMac, it runs excellently, and the SSD drive has the same empty capacity 90GB used out of 480GB.

iMac 21" 2009/late. SSD Kingston 480Gb / macOS 10.12, Sierra.
I configured the SDD as the main startup disk and I transferred all
  the libraries in HDD.


How exactly did you transfer the libraries?!
Note, that Disk Utility.app (if used) does not create a bootable HDD backup!

There are different ways to clone/transfer the entire content of your previous installed main HDD. The following applications will allow exact and bootable drives/disk images.



Option 01: Carbon Cloner creates a bootable drive/volume





Option 02: CloneX4 allows you to make a bootable copy of your startup disk, as well as if you want to change your hard disk. Clone X will create a perfect bootable copy of your startup disk, or of any of your other disks. Clone X automatically handles all settings needed to make a correct bootable copy.