Ztruker is the tech and more than likely knows better than I do. If for whatever reason you're still having issues you can try to reconfigure the EFI Bootloader.
Ztruker, feel free to veto this of course.
If you're willing to give it a shot, let's try for the EFI Bootloader.
1. Boot from the disk and get to the command prompt as you have done previously.
2. Enter the command "diskpart" without the quotes and press enter.
3. There should be a partition that's formatted as FAT32. This is your EFI partition.
4. Assign a drive letter to it and making another attempt at rewriting the boot sector onto the system partition by using the commands:
DISKPART> sel vol 3
DISKPART> assign letter=x:
exit
cd /d x:\EFI\Microsoft\Boot\
bootrec /fixboot
5. Next we're renaming the BCD file with this command:
ren BCD BCD.bak
6. Now we're going to use bcdboot to recreate the BCD with this command:
bcdboot c:\Windows /l en-us /s x: /f ALL
7. Reboot and see where we're at.