The couple I've done recently (2010KDE) took approx 20mins, and although I wasn't looking at CPU usage I don't think it was using anywhere near 100%
I continued browsing and stuff whilst the remaster was being created and I didn't feel any slowing down of my system.
As for excluding folders, 'fraid I don't know the switches/commands to carry that out. You could always move the data in the folders somewhere else and move them back after the cd has been created.
You may of already done this, but I would suggest doing the remaster after a fresh reboot, so you have all your systems resources available to you.