Ugh... So you installed the hack, then ran one of the upgrade scripts but you were already running the latest version? I'm not really sure what would happen, but I don't think it would be good. The scripts aren't that "smart" in the sense of knowing the if any grandular changes have been made or not.
As for font size, it is probably in your CSS declerations, you probably have the size for alt1 different from alt2.
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