su would run calibre as root, and start a new profile for the root user.
This isn't Windows, running things as an administrator isn't required and is only useful for things that are specifically supposed to be run as an administrator -- like user and service management, and installing/updating/removing programs.
Good point on the plugins. calibre lists known installed plugins in customize.py:
plugins = cPickle.loads('stuff')
Just reinstall each plugin. The configuration is the important part, and it is already there.
Or, try copying that file over, and deleting every other line. It might work, depending one what is corrupted and how?
