If it were me I would just put it in there and try to boot it up. It may decide that it's found new hardware (even if it's identical to the old stuff). Let it do it's "new" hardware installation and whatever reboot(s) are necessary. I would pay close attention to attaching everything in the same ports/slots etc as it was on the old board.
You may have to do the robocall to Microsoft for activation. The key here is to (honestly) say "no" if it asks you if the copy of Windows is installed on any other computer.
My MB (a Gigabyte EX58-UD3R) croaked after just under a year of use and I replaced it with the same model just over a year ago. Everything I described above is how it went for me when I replaced it, including booting from the original hardware with Windows already installed. After the phone activation I have had no
problems, either with the new board or with Microsoft pertaining to "Genuine Software" issues.
(And I'm curious to know if you get the "Windows did not properly shut down" message when you start it up for the first time.)