Reconstructing Windows EFI files in /boot partition

Since you have copied all the required files to boot/efi/EFI/Microsoft/Boot, you need to rebuild windows loader configuration. You will need a windows bootable usb or dvd (64 bit will be preferable).

1 : Boot from your bootable medium. Make sure that you are booting in UEFI mode.

2 : At the first screen (where it asks you to choose language and keyboard), press Shift + F10. This will give you a command prompt.

3 : Type diskpartand then list disk (to list all available disks). Select appropriate hard drive by typing select disk #.

4 : Now type list partition and make sure that there is a partition of type system (the efi partition). Select this partition by typing select partition # and assign a temporary drive letter to it, say G by typing assign letter=G.

5 : Just to make sure that drive letter is correctly assigned, type list vol. You should see a volume with drive letter (Ltr) as G & file system (Fs) as FAT32

6 : Close diskpart by typing exit. Make sure that you are in X:\Sources.

7 : Type cd /d G:\EFI\Microsoft\Boot\. Now run these commands one by one.

bootrec /scanos     
bootrec /fixmbr    
bootrec /fixboot
bootrec /rebuildbcd    
bcdboot C:\Windows /l en-us /s G: /f ALL

8 : Close the command prompt and restart the system. You should now be booting into windows.

9 : Of course you may not or don't have the grub menu now. But installing grub is far more easy. Follow any one of these links for more info.