Summary: Solved! The solution is here. Thanks to Nikita Prokopov for telling me how to do this (see comment below). If you want to restore Safari 5.0, you can use this hint or the other method in the comments.
The first thing I after installing Safari 5.1 was to try to fix Reader’s styles. The files were still there, unchanged from my last upgrade, but when I altered them nothing happened. I even deleted the files, and the new Safari Reader kept its default look. I spent a little time digging through all the files I thought could include the preferences, but could not find them. Unless I can find a way to fix this problem, I’m going back to using Readability. If you can find a solution, please tell me!