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The S icon to the left of the Storify, Favorite, Retweet, etc links would look better if the colors were inverted. Having a gray S with no border will better match the #newtwitter design.
Not sure I follow. Could you post a screen grab? Currently the extension matches the light gray of the Twitter icons in the inactive state and uses Storify blue in the active state instead of the dark gray used by the native tweet actions.
You could potentially use a single tweet in multiple Storify stories, so marking a tweet as used with a full color icon mirroring the behavior of favorite and retweet doesn't make much sense for us.
Currently the Storify logo has as solid background with a light S like this. The built in Twitter actions have transparent backgrounds with colored icons like this. My suggestion is to make the S solid colors and the background transparent.