Ok I went back and reread your initial post. I misread you originally. I was fixated that it was your home directory that you were locked out of. If you did not click "set these permissions for subfolders" or however it is worded we should be ok. I don't think you did though, if you had the Users folders would have been reset as well, which they were not. It is possible it killed the system some part of the way through the process though.
Have you tried running repair permissions from the DVD? (Can you repair permissions from the DVD?)
Now unfortunately we are going to have to hunt down what you changed. Much more difficult and given the fact that I like my Mac the way it is I won't try and replicate the issue.
cd /
ls -l is most everything owned by root? If so we are in good shape. If not we have a mess on our hands. let us know and don't bother continuing. You should be fine though since your home directories are were not bollixed. I think you just reset the HD volume link, but am not sure.
cd volumes
ls -l There should be a "Macintosh HD => /" in the list. Who owns it and what is the group? if it is anything but root admin then that is what you changed I think.
chown rootdmin Macintosh\ HD note there is no -R in this command.
Finally make sure permissions are lrwxw-xr-x if not
chmod 755 Macintosh\ HD should fix it.
now
cd /dev then
ls -l disk* are they all owned by root operator? If not do not change them yet. Let us know who they are owned by then we will adjust. Messing with dev is dangerous potentially so we need to make sure we are on the same page.
EDIT: I attached a text file with the permissions of my root folder. That will serve as a baseline for what yours should look like.