reinstalling windows with a different motherboard

my motherboard has gone wonky, and i'm about to get a new one. I wanna know the best way to reinstall Windows with this, so that i get rid of all the old shite and chipset drivers etc... Every other time i've changed motherboard's in the past, i've found that reinstalling windows with the mobo works fine, but it takes about 2 hours to boot up, where as a clean install sorts it out, but i wanna avoid formatting my hard disk? whats the best procedure for this? i'll be using all the same hardware apart from the motherboard.
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  1. OS version?

    <A HREF="http://www.anandtech.com/mysystemrig.html?id=9933" target="_new"> My Rig </A>
  2. i got windows 2000
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