Bruce-- as to which is a better master or slave is difficult for me to speak to because I've yet to "buy the farm", so to speak.
But, as for keeping or deleting Pro Ed., that would be a question of your needs. I've personally kept mine and am running VI from FW drives at the moment until I get my eSATA situation sorted out. It does seem worth the hassle-- if one wants to keep Pro Edition installed-- to set up a worthy HD config. For me it's not how much I'll use PE from here on-- it's the one time I'll NEED to use it that I won't have it which worries me. It's just way too much trouble to reinstall it in a pinch. I'll wait until I have all of the VI Cube up and running-- until the rest of the winds, brass and perc arrive, I'm going to need PE for a while-- and current projects will depend upon PE remaining in place.
One option here is to keep it installed on a second internal HD, and then just replace that internal HD with one that will house part of the VI Cube. You can just store the PE drive in a safe place. Since two drives were recommended for the VI Cube, I'm wondering what your second drive might be if it's not going to be a pair of FW's (is it) or any controller cards? You can put half the Cube on one interal drive, but then...? The second half on an FW? Just curious.
A second internal plus two FW's would be the easiest solution to keep all of VI and PE. If you are running a network of computers, I would think that you might want an HD config that allows all computers to access the library from a central "server".
But if you are convinced that VI has 100% replaced PE for you, then there should be no hesitation with deleting PE altogether. My only advice here is to be 100% certain, otherwise you might regret it... just a thought.