I second Proud
I've always been too chicken to upgrade a distro using the "upgrade" path. I like things nice and fresh
Now, just to answer one of your questions, excluding CD3 would not have caused this problem...I routinely install Mdk9.1 without CD3 (although mind you, it does have a lot of useful stuff on it).
I don't know if KDE or GNOME have log files for themselves but you can take a peek at /var/log and you'll see lots of 'em. Look at your Xfree86.log (something like that) which is the log for Xwindows and you might see some errors there.
forgot to ask...do the other window managers log ok?