when you test the clone target drive to see if it will boot, if it doesn't i'd suggest installing the windows dvd and selecting "repair installation".
If cloning from one sata drive to another, if i don't select the "sector by sector" option at the bottom of the 2nd page (where you select the target drive), then the target drive will not boot and i suspect it's skipped the partition that is un-lettered (or not identified with a letter). Repairing the installation corrects this and afterwards it will boot fine.
Running a sector by sector clone, i've had no isses booting
Note - this only started after i built a new PC with a UEFI BIOS.
Then when i installed a PCIe M.2 SSD, regardless of sector by sector, i need to use the win dvd for a "repair" - and i suspect it has something to do with the fact i'm cloning from a PCIe SSD to a Sata SSD.
to make it less confusing, i'd also suggest downloading and using EaseUS ToDo Backup - much simply user interface - not sure why they include it in their partition manager utility
hope that helps