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Everything explained, and the current stage I'm on, explained in this thread.
While I hate to say this, your best bet is to do a reinstall of Windows.
Windows installations don't do well with changing the motherboard of a system. Many times a repair option, or rather extensive driver reworking can get everything working, but it's just as often that the stability simply isn't there.
The only other thing I can think of offhand would be to see if it will boot correctly in safe-mode. If it will, you may be able to install all your relevent drivers and hopefully that'll address your problems.