How did Gore not win comfortably?

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Gore was basically trailing the entire campaign but closed in the final weeks, aided by the Bush DUI thing and Nader bled to him hardcore late in swing states.

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I remember hearing that Gore would win the Electoral Vote and Bush would win the Popular Vote.

and Bush was prepared to fight that:

http://www.bartcop.com/111tie.htm

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another factor may have been Clinton's low personal favorability ratings.  while a solid majority approved of the job he did a similar majority also personally disliked him, per exits.