Reconstructing Windows EFI files in /boot partition (Linux+Windows dual boot)

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.

link1, link2, link3

Sources : 1, 2, 3, 4.

EDIT - Make sure that you remove the drive letter G assigned to efi partition as soon as possible to keep it from showing up in My Computer.