I just found that "Liscio" theme kit you're talking about, and it seems to work by replacing three obscure system files that contain some of the key GUI art of OS X. They are called "Extras.rsrc", "Extras2.rsrc", and "SArtFile.bin".
The Liscio disk image also contains an uninstaller which appears to (illegally?) contain what might be the original versions of those files from OS X, but they probably came from whatever version of OS X the Liscio guys were using when they developed Liscio.
The "Extras.rsrc" file doesn't seem to exist in Mountain Lion. The "Extras2.rsrc" file in the Liscio uninstaller is correct for Mountain Lion (I guess that file hasn't changed in a while). Unfortunately, the SArtFile.bin file in the Liscio uninstaller is not correct for Mountain Lion. I don't have a Lion machine handy so I can't say whether or not it was right for Lion, but I'm guessing not.
At this point you'll probably need to reinstall Lion in order to get back to the proper Lion versions of those three files. You don't have to reinstall from scratch. You can do an in-place reinstall, which is basically just what some might call a "repair install". I would, however, strongly advise you to make sure you have good backups before you do an in-place reinstall of Lion, just in case.