If only your home dir got messed up you can make a backup copy and then delete it and re-create it. The GUI config files should be re-created the next time you log in so your user account should go back to defaults.
If your permissions on your entire disk got mangled it could be a much bigger problem and will probably be harder to fix, in that case it may be better to backup any files you need and re-install.
Ubuntu has a janitor cleanup program, I'm not sure if that would help.
If you're familiar with the terminal you can chmod the files to the correct permissions and that should take care of the problem.
I am not sure what info I can usefully give - if you would like me to post some log files etc. I would happily do so, if you let me know what to post. I have tried the janitor, which shoudl got rid of some depositaries and I have already chmodded and chgrouped as much as I can - I had to do it in the recovery panel to get pas the first error messages. Now I get no more error messages but cannot log in to the orginal instalation and get logged in to this localhost thing which has no network connection.