Running GUI tools, like
root is Considered Harmful for this reason, among others (hidden functions, ability to silently run program fragments from who knows where, ...).
You don't have a "permission" problem, you have an "ownership" problem.
To find all the files owned by
root (really owned by anybody else), do:
sudo find $HOME \! -user $USER
To change the ownership back to you, you could
sudo chown -R $(id -u):$(id -g) $HOME
but that will change the ownership of all files in and under
sudo find $HOME \! -user $USER >/tmp/list-of-files
# edit the list of files, and delete file files you don't want to chown
xargs sudo chown $(id -u):$(id -g) </tmp/list-of-files
Gives one the opportunity to adjust the list of files, owned by not-you, that will have their ownership changed back to you.