Does anyone else have any thoughts?
As mentioned earlier, bcdboot.
During a clean install Windows setup creates a System partition, after the image (WIM) is applied to the OS partition the bcdboot command copies boot files from the Windows folder to the System partition. If you format the HDD with a single partition the boot files are copied to the root.
If your new HDD only has the single OS partition your copied from your old HDD then run this command from WinPE.
bcdboot c:\windows /s c:
You can get in to WinPE from Windows setup, press shift+F10 or F11, I never remember.
You nay need to change the driver letters to something other than C:. Diskpart and List Volume will show you which driver letter your OS partition is using,