I can't explain why .cshrc would have changed to root ownership - it does sound suspicious. Unfortunately anything you do that is left on the box, he can find out about.
You can generate checksums for your data. It's slow (takes a couple of minutes for just over 4GB of data) but the following generates a file containing md5sum output for all of the files under my home directory and logs it to /tmp/md5sum.log. The output for my 4GB is about 65KB so it's easy to take that off the box and keep it to diff against the output next time:
Code:
echo `date` > /tmp/md5sum.log && find /home/steve -type f -exec sh -c 'md5sum "{}" | sort --key=2 >> /tmp/md5sum.log' \;
40GB of data may take too long, but if not at least you'll know which files have changed.