The easiest way I can think of is to take an image the drive using Acronis, ghost or some equivalent, and then put that image on the drive, telling ti to fill up the amount of space you want it to use ...
No idea why the SSD isn't listed as a boot option. The only thing I can think of is that the BCD on the 4TB drive isn't configured properly, or the boot files didn't get copied properly to the EFI ...
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