Hey Randy,
I've been mulling this question myself. I inherited a backup environment with two master backup servers. Two seperate backup domains, effectively. I, too, am wondering if I should start clean in a new environment. It really depends on how much work you want to do. My recommendation is to upgrade to 6.x mp4. It's a stable release. Or so I'm told by other SEs from Symantec that I've spoken with. So go with that and upgrade your existing catalog as well. I think it would save you a lot of headache in importing tapes down the road. Just my two pennies.
Alex