How could I install Boot Camp drivers to my Windows partition?
Probably your Boot Camp partition is hosed and couldn't be removed simply.
So i would try to reinstall Windows 7 with your pre-made (Microsoft's bootable USB creation tool!) thumb drive.
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Attach the Windows 7 installer thumb drive to your Windows server, format it if necessary (FAT32) and create the bootable Win7 install thumb drive again with the Microsoft tool.
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Download BootCamp5.1.5621 on your server
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Extract BootCamp5.1.5621.zip
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Copy the extracted files and folders ($WinPEDriver$, AutoUnattend.xml, BootCamp etc.) to the root of the thumb drive.
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The file/folder structure in the root of your thumb drive should look like this:
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Detach the thumb drive from your server
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Attach the thumb drive to your Mac
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Reboot your Mac and immediately hold the alt/option button until you see the boot menu
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Choose your thumb drive as boot volume
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Try to reinstall Windows 7. You might have to reformat your existing Windows partition with the disk management tool of the Windows 7 Installer (don't delete or resize it!).
If that doesn't work reboot to Mac OS X, start Boot Camp Assistant and try to remove Windows 7 completely.
If the removal fails check several answers here to remove your Boot Camp partition manually:
remove-windows-7
i-messed-up-the-fusion-drive (both require a Time Machine backup)
or some other answers here.
Before doing that post a comment and i will give advice depending on your partition layout.
Start Boot Camp Assistant from scratch to install Windows 7.