Firstly I am not an old man! Its Grumpy not Gramps!
If I understand 'Van Tokkerns' conversion correctly you need to copy all the files from the 'Gamedata' folder into the same Gamedata folder, so you end up with just the one Gamedata folder!
And just use windows to copy the CD's to your harddrive.
And no it wont be a proper 1:1 copy as it wont play from the DVD! But using a NoCD crack will enable you to play without the need for the DVD in the drive. You just use the DVD to install from therefore allowing you to store the original CD's to a safe place where they wont get damaged from over use.
And lastly your questions concerning DVD conversions should be posted into the CD2DVD thread, thats what its there for.