Actually, I don't the the PH installer does have a built-in uninstaller.
Which files did you trash? According to the PithHelmet web site, you should be able to uninstall it by removing "/Library/Application Support/SIMBL/Plugins/PithHelmet.bundle". I just tried it myself, and it worked.
There are, however, other files that it installs that you might want to remove as well. See the above link for what I think is a full list.
If you don't mind my asking, why do you need to uninstall PithHelmet? If it's because of 10.3.9 incompatibilities, I think the new version 2.4 should fix the problem.
Edit: you might also want to check that directory in both your root-level and user-level Libraries. Maybe it somehow got placed in both.