There are some good links on the Adobe website (forum) about optimizing your PC. I've had some similar problems with CEP Pro 2 also, and am working on it- when I get some time! I'm working a lot right now... but I believe that if you stop at Service Pack 1, you should be allright with all that. Now, maybe that's just true with Win XP, so don't hold me to that for 2000, though 2000 and XP are similar in some ways.
I know a guy who's using Cool Edit Pro 2 with '98, and he reports no problems. If you find a system that works, stick with it! Just passing that along... updates aren't necessarily what you need, and if you're catering to that idea with your system change, you might want to reconsider and not move "up", as it were.
I'm thinking, myself, of moving back to 98...