This is great! We are now one step closer to unraveling this mystery. It looks like there is a
diskutil command somewhere in there which is messing things up as it is receiving malformed input data from somewhere earlier in the script.
This goes hand in hand with the output it generates:
disk1s1
Given the string "disk1", the script will gather all disks that start with a "1" (before the "s" part that denotes the partition) and contain an EFI partition, which in your case are
disk1s1 disk13s2 and
disk14s1, matching up with your original results.
We now have to figure out where exactly the script starts going wrong. To this extent I have attached a slightly modified version of the EFIClone-v3 script that adds additional debug output. I have also completely removed the actual file synchronization part so it's completely safe to run as it has no way of messing with the filesystem anymore.
If you could run this script the same way as before using the Terminal and supply both, the terminal output as well as the newly generated log file, that would be much appreciated