Running GUI tools, like nautilus as 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 $HOME
sudo find $HOME \! -user $USER >/tmp/list-of-files
# edit the list of files, and delete file files you don't want to chown
nano /tmp/list-of-files
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.