On my system (Yosemite 10.10.5), I've noticed that changing Reader.html styles gives no effect. I've inspected the Reader code throug Safari and found that the the only CSS that is linked with Reader is ResourcesWBSReaderSharedStyleSheet.css.
Here is the path to Reader CSS file: /System/Library/PrivateFrameworks/Safari.framework/Versions/A/Resources/...
I've never tried it, but apparently you can modify the file: Safari.app/Contents/Resources/Reader.html
From an Apple community support page:
Do a right-click on the application Safari and choose +Show Package Contents+. An new finder window will open. There is one folder in there named Contents. Contents includes several files and folders, navigate to ...
Here's how you'd do this:
Go into the finder, and drag whichever folder you want to use for this into the "Favorites" section in the sidebar (enable the sidebar in the view menu if it isn't showing).
Run this script, but replace menu item "Xcode" of click menu item "Xcode" of menu 1 of pop up button "Where:" with the name of the folder you added to your ...
I tried mdfind -name Reader.html and on my copy of El Capitan it yields the following path:
So it looks like the file has indeed been moved.