Help with assigning a new boot drive

I am trying to use Windows Recovery Console to assign a new drive as my primary boot. I have installed Windows it boots fine, but I'm experiencing some odd system behavior (like my hard drives won't display in disk management but show up everywhere else).

I was told I could use this GAG utility to fix it, but that didn't work so then it was suggested I use Recovery Console. However I have no idea what I can safely do in that. 'fixmbr' was the only command suggested to me, but that results in a caution message that is a little ominous. Does anyone know what steps I can take to get this done?

The people who were helping me seem to have abandoned the thread I started so I'm starting a new one...see the link below for a more detailed history.

http://www.tomshardware.com/forum/ [...] -managment