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.

Safari Reader is an important feature that Apple added to its Safari web browser in version 5.0. Reader is a built-in tool that as nearly a copy of Arc90’s Readability JavaScript. Reader tries to figure out what part of a webpage is the main text, then removes everything else and applies a simple style to the text. This makes many websites easier to read, particularly on sites with poorly chosen fonts and backgrounds or distracting ads. Glimmer Blocker does a good job with the ads, but something Reader is needed on the sites that use bad styles. Unfortunately, Apple has been moving to blind users with brighter and brighter interfaces, including Safari Reader’s pure black on white on black. That’s fine if you are in a bright room, but otherwise it is annoying and slows reading. Apple doesn’t provide any way to customize the look of Reader other than adjusting the size of the typeface. In Safari 5.0, it only took me a few minutes to figure out how to customize Reader, and I wrote a fairly popular article about how to alter the look of Safari Reader, including how to use ragged-right instead of fully justified text. I expected to need to do this again after the upgrade.

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!

Safari 5.1 also appears to have broken the important BlockTarget Extension, which I wrote about previously.