1. I'm assuming your newly-cloned SSD boot drive boots and functions without any problems. If that's the case you DO NOT HAVE ANY SIGNIFICANT PROBLEM so don't tamper with those E: & F: partitions at this time.
2. Ensure that the SSD boot drive functions properly when your secondary HDD - the 4 TB HDD - is NOT CONNECTED in the system. Assuming the SSD boots & functions properly, then you can reattach the 4 TB HDD. Capiche?
3. You should have provided a screenshot of Disk Management, so do that now. Ensure that the screenshot includes the schematic for all your installed drives as well as the upper portion of DM so as to include the info in the various columns just below the icon menu bar.
4. I'm assuming you're working with the Win 7 OS. Confirm that.